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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
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quant bin failed when making the the heatmap and abundance table #212

Open yuhe4046 opened 5 years ago

yuhe4046 commented 5 years ago

Hi, I used metaWRAP v=1.2.1. I , but quant bin failed when making the the heatmap, and abundance table didn't contain three samples (I have three samples).

Here is my user error:

metawrap quant_bins -o sep_QUANT_BINS -t 40 -a /share/home/yuhe/a/metogenome/0612.SH.ASSEMBLY/final_assembly.fasta -b /share/home/yuhe/data/MY_CHECKM_FOLDER/SH.70.5BIN_REFINEMENT/metawrap_70_5_bins /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R12_1.fastq /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R12_2.fastq /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R13_1.fastq /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R13_2.fastq /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R19_1.fastq /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R19_2.fastq

------------------------------------------------------------------------------------------------------------------------
-----                                  3 forward and 3 reverse read files detected                                 -----
------------------------------------------------------------------------------------------------------------------------

########################################################################################################################
#####                                    SETTING UP OUTPUT AND INDEXING ASSEMBLY                                   #####
########################################################################################################################

------------------------------------------------------------------------------------------------------------------------
-----                            Indexing assembly file with salmon. Ignore any warnings                           -----
------------------------------------------------------------------------------------------------------------------------

Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
index ["sep_QUANT_BINS/assembly_index"] did not previously exist  . . . creating it
[2019-07-22 11:34:07.054] [jLog] [info] building index
[2019-07-22 11:34:07.063] [jointLog] [info] [Step 1 of 4] : counting k-mers
[2019-07-22 11:34:07.331] [jointLog] [warning] Entry with header [k141_5071203_length_501818_cov_27.9845] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.353] [jointLog] [warning] Entry with header [k141_5054086_length_476307_cov_29.5229] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.366] [jointLog] [warning] Entry with header [k141_3427556_length_310886_cov_35.8781] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.378] [jointLog] [warning] Entry with header [k141_3562351_length_272351_cov_24.3273] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.387] [jointLog] [warning] Entry with header [k141_30697_length_268395_cov_28.3423] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.397] [jointLog] [warning] Entry with header [k141_2669835_length_238160_cov_45.0131] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.405] [jointLog] [warning] Entry with header [k141_4108769_length_237011_cov_34.1919] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.412] [jointLog] [warning] Entry with header [k141_2085658_length_223236_cov_77.8299] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.418] [jointLog] [warning] Entry with header [k141_3595791_length_205026_cov_32.1201] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.426] [jointLog] [warning] Entry with header [k141_1133550_length_203510_cov_21.3044] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2019-07-22 11:34:07.432] [jointLog] [warning] Entry with header [k141_4926892_length_201778_cov_52.0528] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
counted k-mers for 950,000 transcriptsElapsed time: 58.9741s

[2019-07-22 11:35:06.043] [jointLog] [info] Replaced 0 non-ATCG nucleotides
[2019-07-22 11:35:06.043] [jointLog] [info] Clipped poly-A tails from 61 transcripts
[2019-07-22 11:35:06.135] [jointLog] [info] Building rank-select dictionary and saving to disk
[2019-07-22 11:35:06.326] [jointLog] [info] done
Elapsed time: 0.19097s
[2019-07-22 11:35:07.205] [jointLog] [info] Writing sequence data to file . . . 
[2019-07-22 11:35:09.059] [jointLog] [info] done
Elapsed time: 1.85373s
[2019-07-22 11:35:14.431] [jointLog] [info] Building 64-bit suffix array (length of generalized text is 2,395,266,018)
[2019-07-22 11:38:05.314] [jointLog] [info] Building suffix array . . . 
success
saving to disk . . . done
Elapsed time: 16.7204s
done
Elapsed time: 680.213s
processed 2,395,000,000 positions[2019-07-22 13:15:55.500] [jointLog] [info] khash had 2,325,282,560 keys
[2019-07-22 13:15:55.531] [jointLog] [info] saving hash to disk . . . 
[2019-07-22 13:22:37.641] [jointLog] [info] done
Elapsed time: 402.11s
[2019-07-22 13:24:11.480] [jLog] [info] done building index

########################################################################################################################
#####                           ALIGNING READS FROM ALL SAMPLES BACK TO BINS WITH SALMON                           #####
########################################################################################################################

------------------------------------------------------------------------------------------------------------------------
-----                                      processing sample SH.R12 with reads                                     -----
-----             /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R12_1.fastq and             -----
-----             /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R12_2.fastq...              -----
------------------------------------------------------------------------------------------------------------------------

### salmon (mapping-based) v0.13.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { sep_QUANT_BINS/assembly_index }
### [ libType ] => { IU }
### [ mates1 ] => { /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R12_1.fastq }
### [ mates2 ] => { /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R12_2.fastq }
### [ output ] => { sep_QUANT_BINS/alignment_files/SH.R12.quant }
### [ meta ] => { }
### [ threads ] => { 40 }
Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
Logs will be written to sep_QUANT_BINS/alignment_files/SH.R12.quant/logs
[2019-07-22 13:24:14.835] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-07-22 13:24:14.835] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Mapping validation is planned to become a default option (i.e. turned on by default) in
the next release of salmon.
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-07-22 13:24:14.835] [jointLog] [info] parsing read library format
[2019-07-22 13:24:14.835] [jointLog] [info] There is 1 library.
[2019-07-22 13:24:14.931] [jointLog] [info] Loading Quasi index
[2019-07-22 13:24:14.931] [jointLog] [info] Loading 64-bit quasi index
[2019-07-22 13:24:14.931] [stderrLog] [info] Loading Suffix Array 
[2019-07-22 13:25:01.014] [stderrLog] [info] Loading Transcript Info 
[2019-07-22 13:25:11.146] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-07-22 13:25:12.737] [stderrLog] [info] There were 956,861 set bits in the bit array
[2019-07-22 13:25:12.979] [stderrLog] [info] Computing transcript lengths
[2019-07-22 13:25:12.982] [stderrLog] [info] Waiting to finish loading hash
[2019-07-22 13:30:51.380] [jointLog] [info] done
[2019-07-22 13:30:51.380] [jointLog] [info] Index contained 956,861 targets
[2019-07-22 13:30:51.380] [stderrLog] [info] Done loading index

processed 94,500,000 fragments
hits: 60,443,475, hits per frag:  0.640319

[2019-07-22 13:36:05.881] [jointLog] [info] Computed 1,099,689 rich equivalence classes for further processing
[2019-07-22 13:36:05.881] [jointLog] [info] Counted 59,999,312 total reads in the equivalence classes 
[2019-07-22 13:36:05.965] [jointLog] [warning] 0.000185788% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.

[2019-07-22 13:36:05.965] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 119,212
[2019-07-22 13:36:05.965] [jointLog] [info] Mapping rate = 63.336%

[2019-07-22 13:36:05.965] [jointLog] [info] finished quantifyLibrary()
[2019-07-22 13:36:06.043] [jointLog] [info] Starting optimizer
[2019-07-22 13:36:06.645] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-07-22 13:36:06.660] [jointLog] [info] iteration = 0 | max rel diff. = 499.942
[2019-07-22 13:36:07.617] [jointLog] [info] iteration = 100 | max rel diff. = 7.83688e-16
[2019-07-22 13:36:07.638] [jointLog] [info] Finished optimizer
[2019-07-22 13:36:07.638] [jointLog] [info] writing output 

------------------------------------------------------------------------------------------------------------------------
-----                                      processing sample SH.R13 with reads                                     -----
-----             /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R13_1.fastq and             -----
-----             /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R13_2.fastq...              -----
------------------------------------------------------------------------------------------------------------------------

### salmon (mapping-based) v0.13.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { sep_QUANT_BINS/assembly_index }
### [ libType ] => { IU }
### [ mates1 ] => { /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R13_1.fastq }
### [ mates2 ] => { /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R13_2.fastq }
### [ output ] => { sep_QUANT_BINS/alignment_files/SH.R13.quant }
### [ meta ] => { }
### [ threads ] => { 40 }
Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
Logs will be written to sep_QUANT_BINS/alignment_files/SH.R13.quant/logs
[2019-07-22 13:36:19.989] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-07-22 13:36:19.989] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Mapping validation is planned to become a default option (i.e. turned on by default) in
the next release of salmon.
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-07-22 13:36:19.989] [jointLog] [info] parsing read library format
[2019-07-22 13:36:19.989] [jointLog] [info] There is 1 library.
[2019-07-22 13:36:20.090] [jointLog] [info] Loading Quasi index
[2019-07-22 13:36:20.090] [jointLog] [info] Loading 64-bit quasi index
[2019-07-22 13:36:20.106] [stderrLog] [info] Loading Suffix Array 
[2019-07-22 13:36:58.424] [stderrLog] [info] Loading Transcript Info 
[2019-07-22 13:37:00.160] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-07-22 13:37:00.481] [stderrLog] [info] There were 956,861 set bits in the bit array
[2019-07-22 13:37:00.637] [stderrLog] [info] Computing transcript lengths
[2019-07-22 13:37:00.641] [stderrLog] [info] Waiting to finish loading hash
[2019-07-22 13:43:47.934] [stderrLog] [info] Done loading index
[2019-07-22 13:43:47.934] [jointLog] [info] done
[2019-07-22 13:43:47.934] [jointLog] [info] Index contained 956,861 targets

processed 96,500,000 fragments
hits: 60,383,942, hits per frag:  0.626929

[2019-07-22 13:49:22.985] [jointLog] [info] Computed 1,106,567 rich equivalence classes for further processing
[2019-07-22 13:49:22.985] [jointLog] [info] Counted 59,623,346 total reads in the equivalence classes 

[2019-07-22 13:49:23.017] [jointLog] [warning] 0.000271435% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.

[2019-07-22 13:49:23.017] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 134,236
[2019-07-22 13:49:23.017] [jointLog] [info] Mapping rate = 61.7705%

[2019-07-22 13:49:23.017] [jointLog] [info] finished quantifyLibrary()
[2019-07-22 13:49:23.085] [jointLog] [info] Starting optimizer
[2019-07-22 13:49:23.667] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-07-22 13:49:23.679] [jointLog] [info] iteration = 0 | max rel diff. = 499.844
[2019-07-22 13:49:24.620] [jointLog] [info] iteration = 100 | max rel diff. = 0.00380135
[2019-07-22 13:49:24.641] [jointLog] [info] Finished optimizer
[2019-07-22 13:49:24.641] [jointLog] [info] writing output 

------------------------------------------------------------------------------------------------------------------------
-----                                      processing sample SH.R19 with reads                                     -----
-----             /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R19_1.fastq and             -----
-----             /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R19_2.fastq...              -----
------------------------------------------------------------------------------------------------------------------------

### salmon (mapping-based) v0.13.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { sep_QUANT_BINS/assembly_index }
### [ libType ] => { IU }
### [ mates1 ] => { /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R19_1.fastq }
### [ mates2 ] => { /share/home/yuhe/a/metogenome/Rawdta/metawrap.clean.data/SH.R19_2.fastq }
### [ output ] => { sep_QUANT_BINS/alignment_files/SH.R19.quant }
### [ meta ] => { }
### [ threads ] => { 40 }
Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
Logs will be written to sep_QUANT_BINS/alignment_files/SH.R19.quant/logs
[2019-07-22 13:49:37.127] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-07-22 13:49:37.127] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Mapping validation is planned to become a default option (i.e. turned on by default) in
the next release of salmon.
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-07-22 13:49:37.127] [jointLog] [info] parsing read library format
[2019-07-22 13:49:37.127] [jointLog] [info] There is 1 library.
[2019-07-22 13:49:37.243] [jointLog] [info] Loading Quasi index
[2019-07-22 13:49:37.243] [jointLog] [info] Loading 64-bit quasi index
[2019-07-22 13:49:37.244] [stderrLog] [info] Loading Suffix Array 
[2019-07-22 13:49:50.533] [stderrLog] [info] Loading Transcript Info 
[2019-07-22 13:49:52.334] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-07-22 13:49:52.662] [stderrLog] [info] There were 956,861 set bits in the bit array
[2019-07-22 13:49:52.829] [stderrLog] [info] Computing transcript lengths
[2019-07-22 13:49:52.833] [stderrLog] [info] Waiting to finish loading hash
[2019-07-22 13:53:12.490] [jointLog] [info] done
[2019-07-22 13:53:12.490] [jointLog] [info] Index contained 956,861 targets
[2019-07-22 13:53:12.490] [stderrLog] [info] Done loading index

processed 88,000,000 fragments
hits: 54,591,362, hits per frag:  0.621314

[2019-07-22 13:58:14.981] [jointLog] [info] Computed 1,074,246 rich equivalence classes for further processing
[2019-07-22 13:58:14.981] [jointLog] [info] Counted 53,970,172 total reads in the equivalence classes 
[2019-07-22 13:58:15.012] [jointLog] [warning] 0.000233768% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.

[2019-07-22 13:58:15.012] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 133,632
[2019-07-22 13:58:15.012] [jointLog] [info] Mapping rate = 61.245%

[2019-07-22 13:58:15.012] [jointLog] [info] finished quantifyLibrary()
[2019-07-22 13:58:15.014] [jointLog] [info] Starting optimizer
[2019-07-22 13:58:15.549] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-07-22 13:58:15.558] [jointLog] [info] iteration = 0 | max rel diff. = 499.75
[2019-07-22 13:58:16.410] [jointLog] [info] iteration = 100 | max rel diff. = 0.00857305
[2019-07-22 13:58:16.431] [jointLog] [info] Finished optimizer
[2019-07-22 13:58:16.431] [jointLog] [info] writing output 

------------------------------------------------------------------------------------------------------------------------
-----                                           summarize salmon files...                                          -----
------------------------------------------------------------------------------------------------------------------------

Starting in: /share/home/yuhe/a/metogenome/0612.SH.ASSEMBLY/sep_QUANT_BINS/alignment_files
Loading counts from: ./SH.R12.quant quant.sf
Loading counts from: ./SH.R13.quant quant.sf
Loading counts from: ./SH.R19.quant quant.sf
"SH.R12.quant.counts",
"SH.R13.quant.counts",
"SH.R19.quant.counts"

########################################################################################################################
#####                                   EXTRACTING AVERAGE ABUNDANCE OF EACH BIN                                   #####
########################################################################################################################

------------------------------------------------------------------------------------------------------------------------
-----                            There were 3 samples detected. Making abundance table!                            -----
------------------------------------------------------------------------------------------------------------------------

------------------------------------------------------------------------------------------------------------------------
-----                   Average bin abundance table stored in sep_QUANT_BINS/abundance_table.tab                   -----
------------------------------------------------------------------------------------------------------------------------

########################################################################################################################
#####                                 MAKING GENOME ABUNDANCE HEATMAP WITH SEABORN                                 #####
########################################################################################################################

------------------------------------------------------------------------------------------------------------------------
-----                                          making heatmap with Seaborn                                         -----
------------------------------------------------------------------------------------------------------------------------

loading libs...
loading abundance data...
drawing clustermap...
Traceback (most recent call last):
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/bin/metawrap-scripts/make_heatmap.py", line 75, in <module>
    draw_clustermap(df, lut)
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/bin/metawrap-scripts/make_heatmap.py", line 58, in draw_clustermap
    g = sns.clustermap(df, figsize=(14,8), col_cluster=True, yticklabels=True, cmap="magma")
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/seaborn/matrix.py", line 1301, in clustermap
    **kwargs)
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/seaborn/matrix.py", line 1128, in plot
    row_linkage=row_linkage, col_linkage=col_linkage)
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/seaborn/matrix.py", line 1029, in plot_dendrograms
    axis=1, ax=self.ax_col_dendrogram, linkage=col_linkage)
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/seaborn/matrix.py", line 747, in dendrogram
    label=label, rotate=rotate)
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/seaborn/matrix.py", line 564, in __init__
    self.linkage = self.calculated_linkage
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/seaborn/matrix.py", line 628, in calculated_linkage
    return self._calculate_linkage_scipy()
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/seaborn/matrix.py", line 603, in _calculate_linkage_scipy
    metric=self.metric)
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/scipy/cluster/hierarchy.py", line 1112, in linkage
    n = int(distance.num_obs_y(y))
  File "/share/home/yuhe/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/scipy/spatial/distance.py", line 2384, in num_obs_y
    raise ValueError("The number of observations cannot be determined on "
ValueError: The number of observations cannot be determined on an empty distance matrix.

************************************************************************************************************************
*****                           something went wrong with making the heatmap. Exiting...                           *****
************************************************************************************************************************

real    145m4.479s
user    349m16.552s
sys 59m31.502s
yuhe4046 commented 5 years ago

here is part of the bin_abundance_table.tab :

Genomic bins    SH
bin.18  2.20254029002
bin.9   0.773597863849
bin.52  0.89788971205
bin.20  1.44597658633
bin.36  2.06748446356
bin.4   1.931248483
bin.25  0.980918497947
bin.22  0.664894156701
bin.6   0.754933941053
bin.27  1.94009149691
bin.15  1.14162389861
bin.70  1.2996628985
yuhe4046 commented 5 years ago

At the same time， I got the following three quant.counts :

 [yuhe@login sep_QUANT_BINS]$ cd quant_files/
 [yuhe@login quant_files]$ ll
total 127440
-rw-rw-r-- 1 yuhe yuhe 43513263 Jul 22 13:58 SH.R12.quant.counts
-rw-rw-r-- 1 yuhe yuhe 43504597 Jul 22 13:58 SH.R13.quant.counts
-rw-rw-r-- 1 yuhe yuhe 43472067 Jul 22 13:58 SH.R19.quant.counts

here is the part of SH.R12.quant.counts:

transcript  count
k141_5071203_length_501818_cov_27.9845  1.44818
k141_5054086_length_476307_cov_29.5229  1.066772
k141_3427556_length_310886_cov_35.8781  1.56786
k141_3562351_length_272351_cov_24.3273  0.995997
k141_30697_length_268395_cov_28.3423    1.473437
k141_2669835_length_238160_cov_45.0131  2.326152
k141_4108769_length_237011_cov_34.1919  1.209103
k141_2085658_length_223236_cov_77.8299  5.532826
k141_3595791_length_205026_cov_32.1201  1.156389
ursky commented 5 years ago

The program cannot make a clustered heatmap from just one column. You need at least 3.

ursky commented 5 years ago

Wait, I just saw the second part of your response. I think what is happening is that the program takes the name of each sample to be everything before a ., so all your samples get abbreviated to be SH. I'll work to fix this bug, but the easiest thing you can probably do in the meantime is changing the names to SH_R12 instead of SH.R12.