Error in step 10

[cmaltec]

Hi, Thanks for putting together SqueezeMeta, it's of great help. I'm running into some issues when running step 14 below is the stdout msg. Any word of wisdom will be appreciated. Cheers K

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

[18 hours, 52 minutes, 10 seconds]: STEP14 -> BINNING: 14.runbinning.pl [E::hts_open_format] Failed to open file /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S058.bam ERROR: fail to open index BAM file '/home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S058.bam' Traceback (most recent call last): File "/home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/concoct_coverage_table.py", line 91, in generate_input_table(args.bedfile, args.bamfiles, samplenames=samplenames) File "/home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/concoct_coverage_table.py", line 41, in generate_input_table sys.stderr.write(out) TypeError: write() argument must be str, not bytes wc: /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/intermediate/binners/concoct/: Is a directory Error running command: /home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/SqueezeMeta/bin/jgi_summarize_bam_contig_depths /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S076.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S082.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S080.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S069.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S042.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S099.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S056.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S075.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S081.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S047.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S066.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S040.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S046.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S065.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S051.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S103.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S096.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S050.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S091.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S045.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S084.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S087.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S059.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S044.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S054.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S060.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S089.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S097.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S078.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S092.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S049.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S104.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S085.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S111.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S098.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S077.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S105.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S095.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S039.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S055.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S057.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S053.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S067.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S064.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S086.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S079.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S041.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S083.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S101.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S073.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S058.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S102.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S109.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S106.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S107.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S094.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S043.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S072.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S108.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S074.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S068.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S070.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S037.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S052.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S071.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S061.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S038.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S088.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S100.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S090.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S110.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S093.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S062.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S048.bam /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S063.bam --outputDepth /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/intermediate/binners/metabat2/contigs.depth.txt.PROV >> /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/syslog 2>&1 at /home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/bin_metabat2.pl line 62. wc: /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/intermediate/binners/metabat2/: Is a directory

[fpusan]

Can you share the project/syslog file with us here?

[cmaltec]

Hi Thank you for your quick response. I apologize I should have sent that right away I attach the zipped file I should also correct what I wrote in the previous message. The error happens at step 10 the issue I've reported was due to a mistake in restarting the analysis without the step and overwrite flags I apologize for the confusion I appreciate your time Christian

On Thu, Mar 14, 2024 at 4:45 AM Fernando Puente-Sánchez < @.***> wrote:

Can you share the project/syslog file with us here?

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/812#issuecomment-1996883544, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIE64KKLOC3NAZSFB3WK2DYYFPS3AVCNFSM6AAAAABEUEHC5GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJWHA4DGNJUGQ . You are receiving this because you authored the thread.Message ID: @.***>

--

Christian Maltecca

Department of Animal Science & Genetics and Genomics Academy Campus Box 7621, Polk Hall 251 Raleigh, NC 27695 Office: (919) 515-0812 Fax: (919) 515-6884 email: @.***

[fpusan]

Glad it was in step 10, then it's closer to other errors we've seen before. I can not see the zipped syslog file here. Can you try attaching it through the github page instead of in your email response?

[cmaltec]

syslog.gz

[fpusan]

Thanks! Do you happen to have the stdout of the original failing run? Does it maybe mention an error running samtools?

[cmaltec]

Ouch, sorry that one has been lost :( I can restart it

[fpusan]

Maybe you can also update to v1.6.3 before restarting. It should be able to restart your current project, and we fixed some issues related to step 10 in that one.

[cmaltec]

Ok, I will try that.

On Thu, Mar 14, 2024 at 11:48 AM Fernando Puente-Sánchez < @.***> wrote:

Maybe you can also update to v1.6.3 before restarting. It should be able to restart your current project, and we fixed some issues related to step 10 in that one.

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/812#issuecomment-1997769255, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIE64MXGUUV5SNRZTHB4JDYYHBFJAVCNFSM6AAAAABEUEHC5GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJXG43DSMRVGU . You are receiving this because you authored the thread.Message ID: @.***>

--

Christian Maltecca

Department of Animal Science & Genetics and Genomics Academy Campus Box 7621, Polk Hall 251 Raleigh, NC 27695 Office: (919) 515-0812 Fax: (919) 515-6884 email: @.***

[cmaltec]

I'm afraid I've created more entropy :) Now after updating I get the following message after running the test install

WARNING: Some SqueezeMeta dependencies could not be found in your environment or failed to execute!

• ERROR: Error running /home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/SqueezeMeta/bin/minimap2 --version

[fpusan]

This shouldn't affect your current run so you can go ahead. I will look into it, may have more questions for you later :)

[cmaltec]

here we go

Reading samples from /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/00.CoassemblyAll.samples Metagenomes found: 75 Reading contig length from /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/intermediate/01.CoassemblyAll.lon Reading orf info from /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/results/03.CoassemblyAll.gff Mapping with Bowtie2 (Langmead and Salzberg 2012, Nat Methods 9(4), 357-9) Creating reference from contigs Working with sample 1: S037 Getting raw reads cp: cannot create regular file '/home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/temp/CoassemblyAll.S037.current_1.gz': Permission denied cp: cannot create regular file '/home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/temp/CoassemblyAll.S037.current_2.gz': Permission denied Aligning to reference with bowtie Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' Error, fewer reads in file specified with -2 than in file specified with -1 terminate called recursively (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) An error occurred during mapping with command /home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/SqueezeMeta/bin/bowtie2/bowtie2 -x /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/CoassemblyAll.bowtie -1 /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/temp/CoassemblyAll.S037.current_1.gz -2 /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/temp/CoassemblyAll.S037.current_2.gz --quiet -p 20 -S /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S037.sam --very-sensitive-local! at /home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/SqueezeMeta/scripts/10.mapsamples.pl line 267, line 0.000000. Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally

For completeness

-r--r--r--. 1 cmaltec NCSU 1410324092 Mar 13 12:07 CoassemblyAll.S037.current_1.gz -r--r--r--. 1 cmaltec NCSU 1035337728 Mar 13 12:07 CoassemblyAll.S037.current_2.gz

==========

[fpusan]

You don't seem to have write permissions in /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/temp Try getting standard rw permissions in your project directory and restarting step 10.

[cmaltec]

apologies but the error persist also, the temp folder has regular read and write permissions below is the stdout

Reading samples from /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/00.CoassemblyAll.samples Metagenomes found: 75 Reading contig length from /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/intermediate/01.CoassemblyAll.lon Reading orf info from /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/results/03.CoassemblyAll.gff Mapping with Bowtie2 (Langmead and Salzberg 2012, Nat Methods 9(4), 357-9) Creating reference from contigs Working with sample 1: S037 Getting raw reads cp: cannot create regular file '/home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/temp/CoassemblyAll.S037.current_1.gz': Permission denied cp: cannot create regular file '/home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/temp/CoassemblyAll.S037.current_2.gz': Permission denied Aligning to reference with bowtie Error, fewer reads in file specified with -2 Error, fewer reads in file specified with -2 than in file specified with -1than in file specified with -1

terminate called recursively terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) An error occurred during mapping with command /home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/SqueezeMeta/bin/bowtie2/bowtie2 -x /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/CoassemblyAll.bowtie -1 /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/temp/CoassemblyAll.S037.current_1.gz -2 /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/temp/CoassemblyAll.S037.current_2.gz --quiet -p 20 -S /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/data/bam/CoassemblyAll.S037.sam --very-sensitive-local! at /home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/SqueezeMeta/scripts/10.mapsamples.pl line 267, line 0.000000. Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally

If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /home/wolftech/cmaltec/NIFA_SqueezeM_CoassemblyAll_01_24_24/CoassemblyAll/syslog file (zip it first) Died at /home/wolftech/cmaltec/mambaforge/envs/SqueezeMeta/bin/SqueezeMeta.pl line 941.

Additionally the samples are indeed created in the temp folder so I'm not sure how to interpret the message thank you

[fpusan]

What's the size of the samples in the temp folder? Do fwd and rev have the same number of reads?

[cmaltec]

1410324092 Mar 13 12:07 CoassemblyAll.S037.current_1.gz 1035337728 Mar 13 12:07 CoassemblyAll.S037.current_2.gz

no they are not

[fpusan]

Can you check if this is also the case for your input files for sample S037? Fwd and rev should have exactly the same number of lines

[cmaltec]

1410324092 S037_QC_R1.fastq.gz 1543018805 S037_QC_R2.fastq.gz These are the QC files. I've used Atlas in a previous analysis (no coassembly), which ended correctly I've used these as input for SqueezeMeta

[fpusan]

SqueezeMeta expects paired end reads to be fully paired (i.e. either both members of the pair are present or they are not). Probably you did QC independently for the fwd and and the rev files, thus making them unpaired.

[cmaltec]

thank you and, i'll start from scratch Apologies for the confusion K

[fpusan]

No problem! I will try to add some checks during pipeline startup so issues like these get detected automatically

[fpusan]

We already check whether the input fastq files are present during pipeline startup, but checking whether they are paired or not would involve uncompressing the files to count the number of lines. This would be a bit hit to execution time for all users, to check for what is a fairly uncommon problem. I have updated the ReadMe instead, adding a reminder to check that files are properly paired, particularly if they have been filtered outside SqueezeMeta