No plots generated

[zmz1988]

Hi, thanks for developing this cool tool! I used merqury.sh command, and it works smoothly, except that no plots were generated. I didn't get any errors while running the command. The mercury tool was installed via miniconda3, and I had build an environment specific for mercury. To solve the problem, I tried copying all the .R and .sh executables into /miniconda3/envs/merqury/bin, and I also tried update all packages in the environment. But still I did not solve the problem. Could you help, please?

Codes are here: merqury.sh sample.meryl sample1.fasta sample_try

Files generated after running the command: sample_try.completeness.stats sample_try.dist_only.hist sample_try.sample1.only.hist sample_try.sample1.qv sample_try.sample1.spectra-cn.hist sample_try.qv sample.hist sample.hist.ploidy sample.filt

[arangrhie]

Hello @zmz1988 ,

Thanks, weird that no plots are generated! Have you checked the log? What does the spectra-cn.log say? Feel free to post the log here.

Best, Arang

[zmz1988]

Hi Arang,

Thanks for replying me! I checked the log and found the warning message:

Found 1 command tree.
Loading required package: argparse
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘argparse’
Loading required package: ggplot2
Loading required package: scales
Error in ArgumentParser(description = "Make spectra-cn plots. Line, filled, and stacked spectra-cn plots will be generated.") : 
  could not find function "ArgumentParser"
Execution halted

But when I tried to install R package argparse in bioconda, it seems that I already have it.

(merqury) [user@server ONT_PB_combine]$ conda install -c bioconda r-argparse
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

[arangrhie]

Hi @zmz1988 , it seems like the required input files aren't completely present from your run. Do you see anything else in the log, above the R log?

[zmz1988]

Hi @arangrhie , thanks for replying me! I actually find it a bit weird, because the memory usage for generating 0.meryl seems like 0 Gb (if I understand it correctly)... But I don't know what's the cause for that, if this is an error.

Anyway, I put the whole log file below, in case you would like to see it.

Usage: spectra-cn.sh <read.meryl> <asm1.fasta> [asm2.fasta] out-prefix
        <read.meryl>    : Generated with meryl count from i.e. illumina wgs reads
        <asm1.fasta>    : haplotype 1 assembly. gzipped or not
        [asm2.fasta]    : haplotype 2 assembly. gzipped or not
        <out-prefix>: output prefix. Required.
                When only <asm1.fasta> is given, results will be generated in haploid mode.
                When <asm2.fasta> is given, results will be generated for each asm1 asm2 haploid asse
mbly and asm1+asm2 diploid assembly.

Detected k-mer size 21

# Get solid k-mers
Generate C.hist

java -jar -Xmx1g /share/apps/miniconda3/envs/merqury/share/merqury/eval/kmerHistToPloidyDepth
.jar C.hist

ploidy  depth   boundary
0       0       26
1       69      76
2       83      123

Filter out kmers <= 26

meryl greater-than 26 output C.gt26.meryl C.meryl

=== Generate spectra-cn plots per assemblies and get QV, k-mer completeness ===

# Generate meryl db for merged_C_necat_ONTR_PBasm_large

# Collect read counts per asm copies
# Read only
# Copy 1 ~ 4
Copy = 1 ..

Copy = 2 ..

Copy = 3 ..

Copy = 4 ..

Copy >4 ..

# Copy numbers in k-mers found only in asm

# Plot C_necat_merge.merged_C_necat_ONTR_PBasm_large.spectra-cn.hist
  Rscript /share/apps/miniconda3/envs/merqury/share/merqury/plot/plot_spectra_cn.R -f C_necat_merge.merged_C_necat_ONTR_PBasm_large.spectra-cn.hist -o C_necat_merge.merged_C_necat_ONTR_PBasm_large.spectra-cn -z C_necat_merge.merged_C_necat_ONTR_PBasm_large.only.hist

# QV statistics

# Per seq QV statistics

# k-mer completeness (recoveray rate) with solid k-mers for merged_C_necat_ONTR_PBasm_large with > 26 counts

# Generate merged_C_necat_ONTR_PBasm_large_only.wig
merged_C_necat_ONTR_PBasm_large_only.wig generated.

No asm2_fa given. Done.
# merged_C_necat_ONTR_PBasm_large only
# Write output
# Get asm only for spectra-asm
#       Plot C_necat_merge.spectra-asm.hist
  Rscript /share/apps/miniconda3/envs/merqury/share/merqury/plot/plot_spectra_cn.R -f C_necat_merge.spectra-asm.hist -o C_necat_merge.spectra-asm -z C_necat_merge.dist_only.hist

# Clean up
Done!
 7   128  P  1006 kB   549 kM   602  S   512 kB   301 MB   301 MB
     8   256  P  1394 kB   274 kM   293  S  1024 kB   293 MB   294 MB
     9   512  P  2184 kB   137 kM   142  S  2048 kB   284 MB   286 MB
    10  1024  P  3784 kB    68 kM    69  S  4096 kB   276 MB   279 MB  Best Value!
    11  2048  P  7008 kB    34 kM    34  S  8192 kB   272 MB   278 MB
    12  4096  P    13 MB    17 kM    17  S    16 MB   272 MB   285 MB
    13  8192  P    25 MB  8795  M     8  S    32 MB   256 MB   281 MB
    14    16 kP    51 MB  4398  M     4  S    64 MB   256 MB   307 MB
    15    32 kP   101 MB  2199  M     2  S   128 MB   256 MB   357 MB
    16    64 kP   202 MB  1100  M     1  S   256 MB   256 MB   458 MB
    17   128 kP   405 MB   550  M     1  S   512 MB   512 MB   917 MB
    18   256 kP   810 MB   275  M     1  S  1024 MB  1024 MB  1834 MB
    19   512 kP  1620 MB   138  M     1  S  2048 MB  2048 MB  3668 MB
    20  1024 kP  3240 MB    69  M     1  S  4096 MB  4096 MB  7336 MB
    21  2048 kP  6480 MB    35  M     1  S  8192 MB  8192 MB    14 GB

FINAL CONFIGURATION
-------------------

Estimated to require 556 MB memory out of 376 GB allowed.
Estimated to require 2 batches.

Configured complex mode for 0.543 GB memory per batch, and up to 2 batches.

Start counting with THREADED method.
Used 0.269 GB / 376.572 GB to store      2097130 kmers; need 0.025 GB to sort        34416 kmers
Used 0.308 GB / 376.572 GB to store     12582759 kmers; need 0.145 GB to sort       202027 kmers
Used 0.356 GB / 376.572 GB to store     25165224 kmers; need 0.247 GB to sort       345172 kmers
Used 0.380 GB / 376.572 GB to store     31453577 kmers; need 0.355 GB to sort       495864 kmers
Used 0.411 GB / 376.572 GB to store     39839808 kmers; need 0.450 GB to sort       629246 kmers
Used 0.451 GB / 376.572 GB to store     50325458 kmers; need 0.542 GB to sort       757843 kmers
Used 0.491 GB / 376.572 GB to store     60811108 kmers; need 0.690 GB to sort       964536 kmers
Used 0.515 GB / 376.572 GB to store     67102498 kmers; need 0.847 GB to sort      1184829 kmers
Used 0.602 GB / 376.572 GB to store     90170886 kmers; need 0.943 GB to sort      1317964 kmers
Used 0.666 GB / 376.572 GB to store    106947905 kmers; need 1.135 GB to sort      1586673 kmers
Used 0.705 GB / 376.572 GB to store    117433555 kmers; need 1.234 GB to sort      1724987 kmers
Used 0.769 GB / 376.572 GB to store    134210574 kmers; need 1.323 GB to sort      1849160 kmers

Input complete.  Writing results to 'merged_C_necat_ONTR_PBasm_large.meryl', using 48 threads.
finishIteration()--

Finished counting.

Cleaning up.

Bye.

Found 1 command tree.

PROCESSING TREE #1 using 48 threads.
  opDifference
    C.meryl
    merged_C_necat_ONTR_PBasm_large.meryl
    output to read.k21.merged_C_necat_ONTR_PBasm_large.0.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

PROCESSING TREE #1 using 48 threads.
  opIntersect
    C.meryl
    opEqualTo
      threshold=1
      merged_C_necat_ONTR_PBasm_large.meryl
    output to read.k21.merged_C_necat_ONTR_PBasm_large.1.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

PROCESSING TREE #1 using 48 threads.
  opIntersect
    C.meryl
    opEqualTo
      threshold=2
      merged_C_necat_ONTR_PBasm_large.meryl
    output to read.k21.merged_C_necat_ONTR_PBasm_large.2.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

PROCESSING TREE #1 using 48 threads.
  opIntersect
    C.meryl
    opEqualTo
      threshold=3
      merged_C_necat_ONTR_PBasm_large.meryl
    output to read.k21.merged_C_necat_ONTR_PBasm_large.3.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

PROCESSING TREE #1 using 48 threads.
  opIntersect
    C.meryl
    opEqualTo
      threshold=4
      merged_C_necat_ONTR_PBasm_large.meryl
    output to read.k21.merged_C_necat_ONTR_PBasm_large.4.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

PROCESSING TREE #1 using 48 threads.
  opIntersect
    C.meryl
    opGreaterThan
      threshold=4
      merged_C_necat_ONTR_PBasm_large.meryl
    output to read.k21.merged_C_necat_ONTR_PBasm_large.gt4.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

PROCESSING TREE #1 using 48 threads.
  opDifference
    merged_C_necat_ONTR_PBasm_large.meryl
    C.meryl
    output to merged_C_necat_ONTR_PBasm_large.0.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.
Loading required package: argparse
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘argparse’
Loading required package: ggplot2
Loading required package: scales
Error in ArgumentParser(description = "Make spectra-cn plots. Line, filled, and stacked spectra-cn plots will be generated.") : 
  could not find function "ArgumentParser"
Execution halted

Found 1 command tree.

Found 1 command tree.
--
-- Estimating memory usage for 'merged_C_necat_ONTR_PBasm_large.0.meryl/'.
--

 p       prefixes             bits gigabytes (allowed: 376 GB)
-- -------------- ---------------- ---------
 6             64          2121056     0.000
 7            128          2072228     0.000
 8            256          2027496     0.000
 9            512          1990956     0.000
10           1024          1970800     0.000 (smallest)
11           2048          1983412     0.000
12           4096          2061560     0.000
13           8192          2270780     0.000 (faster)
14          16384          2742144     0.000
15          32768          3737796     0.000
16          65536          5782024     0.001
17         131072          9923404     0.001
-- -------------- ---------------- ---------
            52924 total kmers

--
-- Minimal memory needed: 0.000 GB
-- Optimal memory needed: 0.000 GB  enabled
-- Memory limit           376.947 GB
--
--
-- Loading kmers from 'merged_C_necat_ONTR_PBasm_large.0.meryl/' into lookup table.
--

For 52924 distinct 21-mers (with 13 bits used for indexing and 29 bits for tags):
    0.000 GB memory for kmer indices -         8192 elements 64 bits wide)
    0.000 GB memory for kmer tags    -        52924 elements 29 bits wide)
    0.000 GB memory for kmer values  -        52924 elements  4 bits wide)
    0.000 GB memory

Will load 52924 kmers.  Skipping 0 (too low) and 0 (too high) kmers.
Allocating space for 69052 suffixes of 29 bits each -> 2002508 bits (0.000 GB) in blocks of 32.000 MB
                     69052 values   of 4 bits each -> 276208 bits (0.000 GB) in blocks of 32.000 MB
Loaded 52924 kmers.  Skipped 0 (too low) and 0 (too high) kmers.
-- Opening input sequences 'merged_C_necat_ONTR_PBasm_large.fasta'.
-- Opening output file '-'.
Bye!

Found 1 command tree.

PROCESSING TREE #1 using 48 threads.
  opIntersect
    merged_C_necat_ONTR_PBasm_large.meryl
    C.gt26.meryl
    output to merged_C_necat_ONTR_PBasm_large.solid.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.
--
-- Estimating memory usage for 'merged_C_necat_ONTR_PBasm_large.0.meryl'.
--

 p       prefixes             bits gigabytes (allowed: 376 GB)
-- -------------- ---------------- ---------
 6             64          2121056     0.000
 7            128          2072228     0.000
 8            256          2027496     0.000
 9            512          1990956     0.000
10           1024          1970800     0.000 (smallest)
11           2048          1983412     0.000
12           4096          2061560     0.000
13           8192          2270780     0.000 (faster)
14          16384          2742144     0.000
15          32768          3737796     0.000
16          65536          5782024     0.001
17         131072          9923404     0.001
-- -------------- ---------------- ---------
            52924 total kmers

--
-- Minimal memory needed: 0.000 GB
-- Optimal memory needed: 0.000 GB  enabled
-- Memory limit           376.947 GB
--
--
-- Loading kmers from 'merged_C_necat_ONTR_PBasm_large.0.meryl' into lookup table.
--

For 52924 distinct 21-mers (with 13 bits used for indexing and 29 bits for tags):
    0.000 GB memory for kmer indices -         8192 elements 64 bits wide)
    0.000 GB memory for kmer tags    -        52924 elements 29 bits wide)
    0.000 GB memory for kmer values  -        52924 elements  4 bits wide)
    0.000 GB memory

Will load 52924 kmers.  Skipping 0 (too low) and 0 (too high) kmers.
Allocating space for 69052 suffixes of 29 bits each -> 2002508 bits (0.000 GB) in blocks of 32.000 MB
                     69052 values   of 4 bits each -> 276208 bits (0.000 GB) in blocks of 32.000 MB
Loaded 52924 kmers.  Skipped 0 (too low) and 0 (too high) kmers.
-- Opening input sequences 'merged_C_necat_ONTR_PBasm_large.fasta'.
-- Opening output file '-'.
Bye!
--
-- Estimating memory usage for 'merged_C_necat_ONTR_PBasm_large.0.meryl'.
--

 p       prefixes             bits gigabytes (allowed: 376 GB)
-- -------------- ---------------- ---------
 6             64          2121056     0.000
 7            128          2072228     0.000
 8            256          2027496     0.000
 9            512          1990956     0.000
10           1024          1970800     0.000 (smallest)
11           2048          1983412     0.000
12           4096          2061560     0.000
13           8192          2270780     0.000 (faster)
14          16384          2742144     0.000
15          32768          3737796     0.000
16          65536          5782024     0.001
17         131072          9923404     0.001
-- -------------- ---------------- ---------
            52924 total kmers

--
-- Minimal memory needed: 0.000 GB
-- Optimal memory needed: 0.000 GB  enabled
-- Memory limit           376.947 GB
--
--
-- Loading kmers from 'merged_C_necat_ONTR_PBasm_large.0.meryl' into lookup table.
--

For 52924 distinct 21-mers (with 13 bits used for indexing and 29 bits for tags):
    0.000 GB memory for kmer indices -         8192 elements 64 bits wide)
    0.000 GB memory for kmer tags    -        52924 elements 29 bits wide)
    0.000 GB memory for kmer values  -        52924 elements  4 bits wide)
    0.000 GB memory

Will load 52924 kmers.  Skipping 0 (too low) and 0 (too high) kmers.
Allocating space for 69052 suffixes of 29 bits each -> 2002508 bits (0.000 GB) in blocks of 32.000 MB
                     69052 values   of 4 bits each -> 276208 bits (0.000 GB) in blocks of 32.000 MB
Loaded 52924 kmers.  Skipped 0 (too low) and 0 (too high) kmers.
-- Opening input sequences 'merged_C_necat_ONTR_PBasm_large.fasta'.
-- Opening output file '-'.
Bye!

Found 1 command tree.

PROCESSING TREE #1 using 48 threads.
  opIntersect
    C.meryl
    merged_C_necat_ONTR_PBasm_large.meryl
    output to read.k21.merged_C_necat_ONTR_PBasm_large.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

Found 1 command tree.
Loading required package: argparse
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘argparse’
Loading required package: ggplot2
Loading required package: scales
Error in ArgumentParser(description = "Make spectra-cn plots. Line, filled, and stacked spectra-cn plots will be generated.") : 
  could not find function "ArgumentParser"
Execution halted

[arangrhie]

Hi @zmz1988 again,

So the R script needs 2 files: C_necat_merge.merged_C_necat_ONTR_PBasm_large.spectra-cn.hist C_necat_merge.merged_C_necat_ONTR_PBasm_large.only.hist

I suspect one (or both?) *.hist file above is empty.

Also, merged_C_necat_ONTR_PBasm_large.0.meryl using 0 memory is also suspicious... This meryl db is used for generating the *.only.hist file. Could you try meryl statistics merged_C_necat_ONTR_PBasm_large.0.meryl | head and post the output?

[zmz1988]

Hi @arangrhie,

I checked the two .hist files you mentioned, and the .spectra-cn.hist file seems fine with lots of lines of data. But the .only.hist has only two lines... I guess this is not good, right?

$  less C_necat_merge.merged_C_necat_ONTR_PBasm_large.only.hist

1       0       52924
2       0       1933
C_necat_merge.merged_C_necat_ONTR_PBasm_large.only.hist (END)

Then I found that there is no merged_C_necat_ONTR_PBasm_large.0.meryl file generated when the command finish running... So the meryl statistics merged_C_necat_ONTR_PBasm_large.0.meryl | head can't run...

[diriano]

Dear Sirs, I am having a similar problem. merqury is not generating plots and several of the output files do not have data/results.

My assembly was generated with hifiasm 0.15.4-r347, separating the two haplotypes of a heterozygous plant genome.

My reads are PacBio HiFi. I created the mery DB as:

meryl count threads=$NSLOTS memory=48g k=19 m64168e_210203_083401.hifi_reads.fasta output pacbioHiFi.meryl

The DB seems to be fine:

meryl statistics pacbioHiFi.meryl/ | head

Found 1 command tree.
Number of 19-mers that are:
  unique              346020850  (exactly one instance of the kmer is in the input)
  distinct            684998550  (non-redundant kmer sequences in the input)
  present           27317177738  (...)
  missing          274192908394  (non-redundant kmer sequences not in the input)

             number of   cumulative   cumulative     presence
              distinct     fraction     fraction   in dataset
frequency        kmers     distinct        total       (1e-6)
--------- ------------ ------------ ------------ ------------

After the "Start counting with THREADED method" there is a badalloc that generated a core dump. this is my merqury command: merqury.sh pacbioHiFi.meryl ../PITFLA_mar_v0.2.bp.hap1.p_ctg.fasta ../PITFLA_mar_v0.2.bp.hap2.p_ctg.fasta PITFLA_mar.v0.2_hap1_2.merqury

And below is my log file. Any help will be greatly appreciate it. Thanks, Diego

Found 1 command tree.

PROCESSING TREE #1 using 1 thread.
  opLessThan
    pacbioHiFi.meryl
    print to (stdout)

Found 1 command tree.
Processing file pacbioHiFi.hist
Start sampling here: 11, 1121205.0
Estimated haploid peak here: 24, 3911082.0
Next max here: 27, 4045030.0
Kick out local maxima: 24, 3911082.0
Next min here: 34, 3475852.0
Next max here: 50, 6459848.0
Stop sampling here: 71, 1087914.0
Running time : 0 h 0 m 1 sec

Found 1 command tree.

PROCESSING TREE #1 using 1 thread.
  opGreaterThan
    threshold=11
    pacbioHiFi.meryl
    output to pacbioHiFi.gt11.meryl

Cleaning up.

Bye.

Found 1 command tree.

Counting 491 (estimated) million canonical 19-mers from 1 input file:
    sequence-file: PITFLA_mar_v0.2.bp.hap1.p_ctg.fasta

SIMPLE MODE
-----------

  19-mers
    -> 274877906944 entries for counts up to 65535.
    -> 4096 Gbits memory used

  515502003 input bases
    -> expected max count of 2062008, needing 6 extra bits.

# Collect read counts per asm copies
# Read only
# Copy 1 ~ 4
Copy = 1 ..

Copy = 2 ..

Copy = 3 ..

Copy = 4 ..

Copy >4 ..

# Copy numbers in k-mers found only in asm
# Union-sum: PITFLA_mar_v0.2.bp.hap1.p_ctg + PITFLA_mar_v0.2.bp.hap2.p_ctg + shared kmer counts (asm)

# k-mer completeness (recovery rate) with solid k-mers for both assemblies with > 11 counts

# 0-counts in the asm; only seen in the reads

# Generate PITFLA_mar.v0.2_hap1_2.merqury.spectra-cn.hist for combined PITFLA_mar_v0.2.bp.hap1.p_ctg.fasta and PITFLA_mar_v0.2.bp.hap2.p_ctg.fasta:
"Is my diploid assembly having k-mers in expected copy numbers?"

Copy = 1 ..

Copy = 1 ..

Copy = 1 ..

Copy = 1 ..

Copy >4 ..

# Count k-mers only seen in the assemblies, not in the reads

# Get asm only for spectra-cn

# Get asm only for spectra-asm

# Plot PITFLA_mar.v0.2_hap1_2.merqury.spectra-cn.hist
Rscript /Storage/progs/merqury/share/merqury/plot/plot_spectra_cn.R -f PITFLA_mar.v0.2_hap1_2.merqury.spectra-cn.hist -o PITFLA_mar.v0.2_hap1_2.merqury.spectra-cn -z PITFLA_mar.v0.2_hap1_2.merqury.only.hist
[1] "x_max: "

# QV

=== Generate spectra-asm.hist for combined PITFLA_mar_v0.2.bp.hap1.p_ctg.fasta and PITFLA_mar_v0.2.bp.hap2.p_ctg.fasta ===
"Is the assembled distinct portion bigger in one of the two assemblies?"
# Get PITFLA_mar_v0.2.bp.hap1.p_ctg / PITFLA_mar_v0.2.bp.hap2.p_ctg / shared kmers

# PITFLA_mar_v0.2.bp.hap1.p_ctg only

# PITFLA_mar_v0.2.bp.hap2.p_ctg only

# shared (PITFLA_mar_v0.2.bp.hap1.p_ctg and PITFLA_mar_v0.2.bp.hap2.p_ctg)

# Write output

Plot PITFLA_mar.v0.2_hap1_2.merqury.spectra-asm.hist
[1] "x_max: "

Clean up

Done!
MB
    20  1024 kP  3240 MB   246  M     1  S  4096 MB  4096 MB  7336 MB
    21  2048 kP  6480 MB   123  M     1  S  8192 MB  8192 MB    14 GB
    22  4096 kP    12 GB    62  M     1  S    16 GB    16 GB    28 GB

FINAL CONFIGURATION
-------------------

Estimated to require 1730 MB memory out of 566 GB allowed.
Estimated to require 2 batches.

Configured complex mode for 1.690 GB memory per batch, and up to 2 batches.

Start counting with THREADED method.
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc

Failed with 'Aborted'; backtrace (libbacktrace):
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
/home/conda/feedstock_root/build_artifacts/ctng-compilers_1610729750655/work/.build/x86_64-conda-linux-gnu/src/gcc/libstdc++-v3/libsupc++/vterminate.cc::95 in _ZN9__gnu_cxx27__verbose_terminate_handlerEv()
/home/conda/feedstock_root/build_artifacts/ctng-compilers_1610729750655/work/.build/x86_64-conda-linux-gnu/src/gcc/libstdc++-v3/libsupc++/eh_terminate.cc::48 in _ZN10__cxxabiv111__terminateEPFvvE()
/home/conda/feedstock_root/build_artifacts/ctng-compilers_1610729750655/work/.build/x86_64-conda-linux-gnu/src/gcc/libstdc++-v3/libsupc++/eh_terminate.cc::58 in _ZSt9terminatev()
/home/conda/feedstock_root/build_artifacts/ctng-compilers_1610729750655/work/.build/x86_64-conda-linux-gnu/src/gcc/libstdc++-v3/libsupc++/eh_throw.cc::95 in __cxa_throw()
/home/conda/feedstock_root/build_artifacts/ctng-compilers_1610729750655/work/.build/x86_64-conda-linux-gnu/src/gcc/libstdc++-v3/libsupc++/new_op.cc::54 in _Znwm()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
/Storage/progs/merqury/share/merqury/eval/spectra-cn.sh: line 64: 176012 Abortado                (imagem do núcleo gravada)meryl count k=$k output ${asm}.meryl $asm_fa
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.PITFLA_mar_v0.2.bp.hap1.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.PITFLA_mar_v0.2.bp.hap1.p_ctg.1.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.PITFLA_mar_v0.2.bp.hap1.p_ctg.2.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.PITFLA_mar_v0.2.bp.hap1.p_ctg.3.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.PITFLA_mar_v0.2.bp.hap1.p_ctg.4.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.PITFLA_mar_v0.2.bp.hap1.p_ctg.gt4.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
/Storage/progs/merqury/share/merqury/eval/spectra-cn.sh: line 111: -: syntax error: operand expected (error token is "-")
rm: não foi possível remover “read.k19.PITFLA_mar_v0.2.bp.hap2.p_ctg.0.meryl”: Arquivo ou diretório não encontrado
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
Can't interpret 'PITFLA_mar_v0.2.bp.hap2.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg_union.meryl': not a meryl command, option, or recognized input file.

Found 1 command tree.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg.solid.meryl': not a meryl command, option, or recognized input file.
awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg_union.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.0.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg_union.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.1.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg_union.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.2.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg_union.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.3.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg_union.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.4.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg_union.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.gt4.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg_union.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
Can't interpret 'PITFLA_mar_v0.2.bp.hap2.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
Can't interpret 'PITFLA_mar_v0.2.bp.hap2.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap2.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_or_PITFLA_mar_v0.2.bp.hap2.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_or_PITFLA_mar_v0.2.bp.hap2.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
/Storage/progs/merqury/share/merqury/eval/spectra-cn.sh: line 208: -: syntax error: operand expected (error token is "-")
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.0.only.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap2.p_ctg.0.only.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_and_PITFLA_mar_v0.2.bp.hap2.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
Carregando pacotes exigidos: argparse
Carregando pacotes exigidos: ggplot2
Carregando pacotes exigidos: scales
Error in `[.data.frame`(dat_0, , 3) : undefined columns selected
Calls: spectra_cn_plot -> [ -> [.data.frame
Além disso: Warning message:
In max(dat[dat[, 1] != "read-total" & dat[, 1] != "read-only" &  :
  nenhum argumento não faltante para max; retornando -Inf
Execução interrompida
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_or_PITFLA_mar_v0.2.bp.hap2.p_ctg.0.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_PITFLA_mar_v0.2.bp.hap2.p_ctg_union.meryl': not a meryl command, option, or recognized input file.
awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted
awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted
rm: não foi possível remover “PITFLA_mar_v0.2.bp.hap2.p_ctg.0.meryl”: Arquivo ou diretório não encontrado
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap2.p_ctg.meryl': not a meryl command, option, or recognized input file.
Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
Can't interpret 'PITFLA_mar_v0.2.bp.hap2.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
Can't interpret 'PITFLA_mar_v0.2.bp.hap2.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_only.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap2.p_ctg_only.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'PITFLA_mar_v0.2.bp.hap1.p_ctg_shrd.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.0.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.PITFLA_mar_v0.2.bp.hap1.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.PITFLA_mar_v0.2.bp.hap2.p_ctg.meryl': not a meryl command, option, or recognized input file.
usage: meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    print                display kmers on the screen as 'kmercount'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=              create mers of size K bases (mandatory).
      n=              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, subtracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

Can't interpret 'read.k19.shrd.meryl': not a meryl command, option, or recognized input file.
Carregando pacotes exigidos: argparse
Carregando pacotes exigidos: ggplot2
Carregando pacotes exigidos: scales
Error in `[.data.frame`(dat_0, , 3) : undefined columns selected
Calls: spectra_cn_plot -> [ -> [.data.frame
Além disso: Warning message:
In max(dat[dat[, 1] != "read-total" & dat[, 1] != "read-only" &  :
  nenhum argumento não faltante para max; retornando -Inf
Execução interrompida

[diriano]

Well I did to changes in the way I ran merqury that let merqury run to completion without complains, and generating all output files, including graphics. So here it is what I did:

1. I was using meryl DB and assembly fasta files that were in other folders (outside where I was running merqury). I did a sym link of the meryl DBs to the folder where I ran Merqury, and copied the fasta files to the same folder.
2. Before I was running merqury without setting up OMP_NUM_THREADS, so merqury was using all my 56 cores. This time I set it up at 4 cores/threads, like this:

OMP_NUM_THREADS=4
export OMP_NUM_THREADS

3. In most of the merqury bash scripts I changed the shebang to look like #!/bin/bash -l, to avoid a problem by using the module system (triggered by the load of $MERQURY/util/util.sh
4. Some of the merqury bash scripts had a space in the shebang, I deleted it.

Hope this helps.

[shaferab]

thanks @diriano I was having identical issues your suggested fixes resolved them. Much appreciated you following up.

[mictadlo]

Hello, I created a new bioconda recipe, but I can not merge it yet because version 1.3 already exists. Could you please create version 1.4?

Thank you in advance,

Best wishes,

Michal