ls: cannot access 'mapped.*.bed': No such file or directory

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Gracy Buckholtz

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Aug 17, 2023, 5:51:36 PM8/17/23

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Hi everyone,

I am new to bioinformatics and job submission. I have been stuck trying to debug the error in the subject line which is output righ as FreeBayes is about to start:

ls: cannot access 'mapped.*.bed': No such file or directory

I noticed that seems to be a common issue but I haven't found any thread that seems to have the same issues I am having. I have tried a few different things: rerunning assembly, submitting the SNP call job with more memory, and trying to call SNPs on a smaller set of samples, and I am at a bit of a loss.

This is the last output of my dDocent.runs file. This is from a smaller subset of data but I was getting the same error when running on the entire set.

"Now sit back, relax, and wait for your analysis to finish

Genomic interval creation completed successfully.

Using FreeBayes to call SNPs

Using existing popmap file

ls: cannot access 'mapped.*.bed': No such file or directory

rm: cannot remove 'mapped.*.bed': No such file or directory

vcfcombine: symbol lookup error: /scratch/gracyb/home/gracyb/scratch/miniconda3/envs/ddocent_env/bin/../lib/libvcflib.so.1: undefined symbol: wavefront_align

mv: cannot stat 'raw.*.vcf': No such file or directory

Using VCFtools to parse TotalRawSNPS.vcf for SNPs that are called in at least 90% of individuals

dDocent has finished with an analysis in /home/gracyb/scratch/dDocent_tests

dDocent started Thu Aug 17 14:22:06 PDT 2023

dDocent finished Thu Aug 17 14:22:11 PDT 2023

After filtering, kept 0 out of a possible 0 Sites

dDocent 2.9.4

The 'd' is silent, hillbilly"

I used process radtags for demultiplexing and checked the sequences put out from there with the command head and they seem normal. I ran the assembly twice and the runs were identical. The output from read mapping seems normal. Each sample has a .bam and a .bai file and the logfiles folder is full of .bam.log and bwa.*.log files that all show:

[M::main_mem] mean insert size: 294.000, stddev: 58.000, max: 394, min: 194

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 2225928 sequences (320000282 bp)...

[M::mem_process_seqs] Processed 2225928 reads in 303.404 CPU sec, 19.020 real sec

[M::process] read 2229616 sequences (320000075 bp)...

[M::mem_process_seqs] Processed 2229616 reads in 283.995 CPU sec, 9.579 real sec

[M::process] read 2128842 sequences (306306201 bp)...

[M::mem_process_seqs] Processed 2128842 reads in 277.708 CPU sec, 8.902 real sec

[main] Version: 0.7.17-r1188

[main] CMD: bwa mem -L 20,5 -I 294,58,394,194 -t 32 -a -M -T 10 -A 1 -B 4 -O 6 -R @RG\tID:376_81\tSM:376_81\tPL:Illumina reference.fasta 376_81.R1.fq.gz 376_81.R2.fq.gz

[main] Real time: 60.958 sec; CPU: 891.118 sec

One potential error that I did notice is that all of the bwa.*.log files seem the same. They have different names based on the samples but using the cat function shows that they all contain the same mean insert size. This is not simulated data. Could this be a part of the issue?

I've attached the log as a file to this post. Here is my working directory:

total 22149982

-rw-r--r-- 1 gracyb gracyb 0 Aug 17 13:37 306_40.cov.stats

-rw-r--r-- 1 gracyb gracyb 142752801 Aug 17 12:43 306_40.F.fq.gz

-rw-r--r-- 1 gracyb gracyb 143781938 Aug 17 12:43 306_40.R1.fq.gz

-rw-r--r-- 1 gracyb gracyb 161232363 Aug 17 12:43 306_40.R2.fq.gz

-rw-r--r-- 1 gracyb gracyb 159215971 Aug 17 12:43 306_40.R.fq.gz

-rw-r--r-- 1 gracyb gracyb 117121250 Aug 17 12:43 306_40-RG.bam

-rw-r--r-- 1 gracyb gracyb 1514512 Aug 17 12:43 306_40-RG.bam.bai

-rw-r--r-- 1 gracyb gracyb 0 Aug 17 13:37 317.330_101.cov.stats

-rw-r--r-- 1 gracyb gracyb 95647436 Aug 17 12:43 317.330_101.F.fq.gz

-rw-r--r-- 1 gracyb gracyb 99839628 Aug 17 12:43 317.330_101.R1.fq.gz

-rw-r--r-- 1 gracyb gracyb 108022789 Aug 17 12:43 317.330_101.R2.fq.gz

-rw-r--r-- 1 gracyb gracyb 103240769 Aug 17 12:43 317.330_101.R.fq.gz

-rw-r--r-- 1 gracyb gracyb 58779170 Aug 17 12:43 317.330_101-RG.bam

-rw-r--r-- 1 gracyb gracyb 1800640 Aug 17 12:43 317.330_101-RG.bam.bai

-rw-r--r-- 1 gracyb gracyb 0 Aug 17 13:37 318_111.cov.stats

-rw-r--r-- 1 gracyb gracyb 208498347 Aug 17 12:43 318_111.F.fq.gz

-rw-r--r-- 1 gracyb gracyb 217298975 Aug 17 12:43 318_111.R1.fq.gz

-rw-r--r-- 1 gracyb gracyb 237937714 Aug 17 12:43 318_111.R2.fq.gz

-rw-r--r-- 1 gracyb gracyb 227475037 Aug 17 12:43 318_111.R.fq.gz

-rw-r--r-- 1 gracyb gracyb 122874972 Aug 17 12:43 318_111-RG.bam

-rw-r--r-- 1 gracyb gracyb 1960408 Aug 17 12:43 318_111-RG.bam.bai

-rw-r--r-- 1 gracyb gracyb 0 Aug 17 13:37 403_114.cov.stats

-rw-r--r-- 1 gracyb gracyb 68122731 Aug 17 12:43 403_114.F.fq.gz

-rw-r--r-- 1 gracyb gracyb 70843645 Aug 17 12:43 403_114.R1.fq.gz

-rw-r--r-- 1 gracyb gracyb 77578300 Aug 17 12:43 403_114.R2.fq.gz

-rw-r--r-- 1 gracyb gracyb 74178723 Aug 17 12:43 403_114.R.fq.gz

-rw-r--r-- 1 gracyb gracyb 44859117 Aug 17 12:43 403_114-RG.bam

-rw-r--r-- 1 gracyb gracyb 1796104 Aug 17 12:43 403_114-RG.bam.bai

-rw-r--r-- 1 gracyb gracyb 0 Aug 17 13:37 AG_30A10.cov.stats

-rw-r--r-- 1 gracyb gracyb 62626930 Aug 17 12:43 AG_30A10.F.fq.gz

-rw-r--r-- 1 gracyb gracyb 63329590 Aug 17 12:43 AG_30A10.R1.fq.gz

-rw-r--r-- 1 gracyb gracyb 70611429 Aug 17 12:43 AG_30A10.R2.fq.gz

-rw-r--r-- 1 gracyb gracyb 69412703 Aug 17 12:43 AG_30A10.R.fq.gz

-rw-r--r-- 1 gracyb gracyb 58149428 Aug 17 12:43 AG_30A10-RG.bam

-rw-r--r-- 1 gracyb gracyb 1373320 Aug 17 12:43 AG_30A10-RG.bam.bai

-rw-r--r-- 1 gracyb gracyb 79 Aug 17 14:22 bamlist.list

-rw-r--r-- 1 gracyb gracyb 21774619021 Aug 17 12:43 cat-RRG.bam

-rw-r--r-- 1 gracyb gracyb 2398816 Aug 17 12:43 cat-RRG.bam.bai

-rw-r----- 1 gracyb gracyb 0 Aug 17 14:22 cov.split.stats

-rw-r----- 1 gracyb gracyb 0 Aug 17 13:37 cov.stats

-rw-r----- 1 gracyb gracyb 4935 Aug 17 14:22 dDocent_main.LOG

-rw-r----- 1 gracyb gracyb 1443 Aug 17 14:22 dDocent.runs

-rw-r----- 1 gracyb gracyb 39 Aug 17 14:22 Final.recode.vcf

-rw-r----- 1 gracyb gracyb 0 Aug 17 13:37 genome.file

drwxr-x--- 2 gracyb gracyb 4096 Aug 17 14:22 logfiles

-rw-r----- 1 gracyb gracyb 0 Aug 17 13:37 mapped.bed

-rw-r----- 1 gracyb gracyb 44 Aug 17 14:22 namelist

-rw-r----- 1 gracyb gracyb 67 Aug 17 13:37 popmap

drwxr-x--- 2 gracyb gracyb 4096 Aug 17 14:12 raw.vcf

-rw-r--r-- 1 gracyb gracyb 9351734 Aug 17 12:43 reference.fasta

-rw-r--r-- 1 gracyb gracyb 1021402 Aug 17 14:08 reference.fasta.amb

-rw-r--r-- 1 gracyb gracyb 1304571 Aug 17 14:08 reference.fasta.ann

-rw-r--r-- 1 gracyb gracyb 8673148 Aug 17 14:08 reference.fasta.bwt

-rw-r--r-- 1 gracyb gracyb 1214871 Aug 17 14:08 reference.fasta.fai

-rw-r--r-- 1 gracyb gracyb 2168266 Aug 17 14:08 reference.fasta.pac

-rw-r--r-- 1 gracyb gracyb 4336584 Aug 17 14:08 reference.fasta.sa

-rw-r----- 1 gracyb gracyb 2563 Aug 17 13:37 SNP_call_aug17.out

-rw-r--r-- 1 gracyb gracyb 423 Aug 17 12:48 SNPcalling_only_config.file

-rw-r--r-- 1 gracyb gracyb 272 Aug 17 12:47 SNPcall_only_aug17_job.sh

-rw-r----- 1 gracyb gracyb 0 Aug 17 14:22 TotalRawSNPs.vcf

Please let me know if there is any other information that I could provide that would be helpful or any other resources I should check for help with this.

Thank you,

Gracy

dDocent_main.LOG

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