Error Using Docker

[danphillips28]

Hi! I am trying to run MAX on my own data and have run into some issues. I was hoping to get to help.

I am using the Docker method. I have already successfully run the test data as follows:

bash runMAXdocker.sh -param test_params.sh

I then generated a new params file pointing towards my own mutation list, gtf and transcript files, and an (fastq) input directory (on an external hard drive). I then call to MAX similarly to before, but get an error I don´t understand:

bash runMAXdocker.sh -param test_params_LMNA.sh 

---------------------------------------------------------------------------
                     You are running MAX v0.2.0 using docker ....
---------------------------------------------------------------------------

Loading parameters from file...
Mutation file is:/source/referenceDB/mutation_list.txt
GFT file is:/source/referenceDB/WT_transcript.gtf
Wild-type reference is:/source/referenceDB/WT_transcripts.fa
hg version is:hg38
Working directory is:/source/output
Number of threads:4

Number of arguments:  5
List of arguments:  mut=/source/referenceDB/mutation_list.txt gtf=/source/referenceDB/WT_transcript.gtf ref=/source/referenceDB/WT_transcripts.fa workdir=/source/output hg=hg38 

Attaching package: 'data.table'

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: Link to the source
# Organism: Homo sapiens
# Taxonomy ID: 9606
# miRBase build ID: NA
# Genome: NA
# transcript_nrow: 42
# exon_nrow: 114
# cds_nrow: 33
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2024-06-23 21:13:32 +0000 (Sun, 23 Jun 2024)
# GenomicFeatures version at creation time: 1.38.2
# RSQLite version at creation time: 2.2.9
# DBSCHEMAVERSION: 1.2

Sqlite file generated
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  In range 1: at least two out of 'start', 'end', and 'width', must
  be supplied.
Calls: GRanges -> IRanges -> solveUserSEW0 -> .Call2
Execution halted
cat: Mutant3.fa: No such file or directory
rm: cannot remove 'Mutant3.fa': No such file or directory
rm: cannot remove 'Mutant2.fa': No such file or directory

 WT_Mut.fa is generated. 

Number of arguments:  2
List of arguments:  WT_Mut_reference.fa /source/output 
Loading required package: polyester
---------------------------------------------------------------

--- MAX acknowledges the Sailfish and Rapmap for this indexer ---

---------------------------------------------------------------

writing log to Index_reference/LogDir/MAX_index.log
RapMap Indexer

[Step 1 of 4] : counting k-mers
Elapsed time: 0.00300248s

Replaced 0 non-ATCG nucleotides
Clipped poly-A tails from 1 transcripts
Building rank-select dictionary and saving to disk done
Elapsed time: 0.00176736s
Writing sequence data to file . . . done
Elapsed time: 0.0028684s
[info] Building 32-bit suffix array (length of generalized text is 78852)
Building suffix array . . . success
saving to disk . . . done
Elapsed time: 0.00533821s
done
Elapsed time: 0.0206044s
processed 0 positions
khash had 8812 keys
saving hash to disk . . . done
Elapsed time: 0.0171321s
Logs will be written to /source/output/LogDir
[2024-06-23 21:16:14.801] [jointLog] [info] parsing read library format
there is 1 lib
Loading 32-bit quasi index[2024-06-23 21:16:14.837] [jointLog] [info] Loading Quasi index
[2024-06-23 21:16:14.848] [jointLog] [info] done
Index contained 42 targets
Loaded targets

[2024-06-23 21:16:14.842] [stderrLog] [info] Loading Suffix Array 
[2024-06-23 21:16:14.843] [stderrLog] [info] Loading Transcript Info 
[2024-06-23 21:16:14.844] [stderrLog] [info] Loading Rank-Select Bit Array
[2024-06-23 21:16:14.845] [stderrLog] [info] Successfully loaded position hash
[2024-06-23 21:16:14.847] [stderrLog] [info] There were 42 set bits in the bit array
[2024-06-23 21:16:14.848] [stderrLog] [info] Computing transcript lengths
[2024-06-23 21:16:14.848] [stderrLog] [info] Waiting to finish loading hash
processed 1500000 fragmentsstderrLog] [info] Done loading index
hits: 26019464, hits per frag (may not be concordant):  17.3497
[2024-06-23 21:16:46.120] [jointLog] [info] Gathered fragment lengths from all threads
[2024-06-23 21:16:46.124] [jointLog] [info] Building empirical fragment length distribution
[2024-06-23 21:16:46.124] [jointLog] [info] finished building empirical fragment length distribution
[2024-06-23 21:16:46.125] [jointLog] [info] Estimating effective lengths
[2024-06-23 21:16:46.125] [jointLog] [info] Emp. dist min = 0, Emp. dist max = 999
Done Quasi-Mapping 

=========================================================================

[MAX] -- We are export some data here -- 

=========================================================================

[MAX] -- Export fragment information 

Read length 100 fragLengthMedian 250 fragLengthMean 250.438 fragLengthSd 24.5837Observed Fragments 1589841 Mapped Fragments 1589617 Total hits 26848572 kmer 31

[MAX] -- Extracting equivalence class 

[2024-06-23 21:16:46.153] [jointLog] [info] Computed 217 rich equivalence classes for further processing
[2024-06-23 21:16:46.153] [jointLog] [info] Counted 1589617 total reads in the equivalence classes 
[2024-06-23 21:16:46.154] [jointLog] [info] Start to export equivalence classes:

[2024-06-23 21:16:46.267] [jointLog] [info] Finished exporting equivalence classes

Number of arguments:  3
List of arguments:  in=Mutated_Combined_eqclass.txt out=/source/output/X_matrix.RData workdir=/source/output 

 buildCRP.R will run with the following parameter setting: 
 ----------------------------------------------------- 
 in:  Mutated_Combined_eqclass.txt
 out:  /source/output/X_matrix.RData
 workdir:  /source/output
 ----------------------------------------------------- Loading required package: iterators
Loading required package: parallel
   user  system elapsed 
  0.057   0.010   0.561 
   user  system elapsed 
  0.103   0.026   0.200 

X matrix is generated

rm: cannot remove 'wild_type_subset_genes.fa': No such file or directory

Number of arguments:  3
List of arguments:  workdir=/source/output design.matrix=X_matrix.RData core=4 

 Create_count_matrix.R will run with the following parameter setting: 
 ----------------------------------------------------- 
 workdir:  /source/output
 core:  4
 design.matrix:  X_matrix.RData
 ----------------------------------------------------- Error in file(file, "rt") : invalid 'description' argument
Calls: read.table -> file
Execution halted

Number of arguments:  4
List of arguments:  workdir=/source/output design.matrix=X_matrix.RData max.out=MAX_isoform_expression.RData core=4 

 AEM_update_X_beta.R will run with the following parameter setting: 
 ----------------------------------------------------- 
 workdir:  /source/output
 core:  4
 design.matrix:  X_matrix.RData
 max.out:  MAX_isoform_expression.RData
 remove.ycount:  TRUE
 ----------------------------------------------------- Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'Ycount.RData', probable reason 'No such file or directory'
Execution halted

Where should I start? Anything obvious to you? Happy to send input file (excluding the fastq files, which are trimmed with trimGalore!).

Hope you can help!

Thanks in advance, Daniel

[nghiavtr]

Hi @danphillips28 ,

Thank you for using MAX.

From your logs, it is likely that there is some issue with your annotation files. Please send us the annotation files and fastq files with the scripts that we can reproduce the errors. We will check the issues as soon as we can.

Best, Nghia

[danphillips28]

Thanks! Can you provide an email? I couldn't find it.

[nghiavtr]

please send the files to TrungNghia.Vu@ki.se

Nghia