Closed poddarharsh15 closed 3 months ago
Hi @poddarharsh15,
It looks like you are trying to use the current directory as the temp directory .
. You will need to add -x
to your command to overwrite any temp files
Thank you for quick reply can I modify command line like this:-
dysgu run \\
-p ${task.cpus} \\
-x \\
$fasta \\
. \\
$input_bam \\
| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz
tabix ${args3} ${prefix}.vcf.gz
Is this okay?
Yes!
I am running the above mentioned command line, still I am not able to emit any outputs Could you please have a look at the log file, Thanks.
Input bam
2024-06-25 11:36:07,112 [INFO ] [dysgu-run] Version: 1.6.2 2024-06-25 11:36:07,112 [INFO ] run -p 2 -x genome.fasta . test.paired_end.recalibrated.sorted.bam 2024-06-25 11:36:07,112 [INFO ] Destination: . 2024-06-25 11:36:07,382 [INFO ] dysgu fetch test.paired_end.recalibrated.sorted.bam written to ./test.paired_end.recalibrated.sorted.dysgu_reads.bam, n=252, time=0:00:00 h:m:s 2024-06-25 11:36:07,382 [INFO ] Input file is: ./test.paired_end.recalibrated.sorted.dysgu_reads.bam [W::hts_idx_load3] The index file is older than the data file: test.paired_end.recalibrated.sorted.bam.bai 2024-06-25 11:36:07,385 [INFO ] Sample name: normal 2024-06-25 11:36:07,385 [INFO ] Writing vcf to stdout 2024-06-25 11:36:07,385 [INFO ] Running pipeline 2024-06-25 11:36:07,552 [INFO ] Calculating insert size. Removed 0 outliers with insert size >= 1359.0 2024-06-25 11:36:07,563 [INFO ] Inferred read length 100.0, insert median 351, insert stdev 145 2024-06-25 11:36:07,564 [INFO ] Max clustering dist 1076 2024-06-25 11:36:07,564 [INFO ] Building graph with clustering 1076 bp 2024-06-25 11:36:07,566 [INFO ] Total input reads 252 2024-06-25 11:36:07,566 [INFO ] Graph constructed 2024-06-25 11:36:07,566 [INFO ] Minimum support 3 2024-06-25 11:36:07,602 [CRITICA] No events found 2024-06-25 11:36:07,602 [INFO ] dysgu run test.paired_end.recalibrated.sorted.bam complete, time=0:00:00 h:m:s
Input cram
2024-06-25 11:36:18,595 [INFO ] [dysgu-run] Version: 1.6.2 2024-06-25 11:36:18,595 [INFO ] run -p 2 -x genome.fasta . test.paired_end.recalibrated.sorted.cram 2024-06-25 11:36:18,595 [INFO ] Destination: . 2024-06-25 11:36:19,056 [INFO ] dysgu fetch test.paired_end.recalibrated.sorted.cram written to ./test.paired_end.recalibrated.sorted.dysgu_reads.bam, n=252, time=0:00:00 h:m:s 2024-06-25 11:36:19,057 [INFO ] Input file is: ./test.paired_end.recalibrated.sorted.dysgu_reads.bam 2024-06-25 11:36:19,058 [INFO ] Sample name: normal 2024-06-25 11:36:19,058 [INFO ] Writing vcf to stdout 2024-06-25 11:36:19,058 [INFO ] Running pipeline 2024-06-25 11:36:19,509 [INFO ] Calculating insert size. Removed 0 outliers with insert size >= 1359.0 2024-06-25 11:36:19,519 [INFO ] Inferred read length 100.0, insert median 351, insert stdev 145 2024-06-25 11:36:19,520 [INFO ] Max clustering dist 1076 2024-06-25 11:36:19,520 [INFO ] Building graph with clustering 1076 bp 2024-06-25 11:36:19,522 [INFO ] Total input reads 252 2024-06-25 11:36:19,522 [INFO ] Graph constructed 2024-06-25 11:36:19,522 [INFO ] Minimum support 3 2024-06-25 11:36:19,556 [CRITICA] No events found 2024-06-25 11:36:19,556 [INFO ] dysgu run test.paired_end.recalibrated.sorted.cram complete, time=0:00:00 h:m:s
The log suggests only 252 reads were in your test.paired_end.recalibrated.sorted.cram file, is this correct?
252
Yes it is correct because these are the test_samples which are extremely small size. <300kb
Perhaps there are no SVs present? Alternatively you can try adjusting the min-support parameter, it is set at 3 by default for paired-end reads.
Probably yes I was running on other test_samples which are a bit larger in size and dysgu was successfully able to detect SVs,
--min-support TEXT Minimum number of reads per SV [default: 3]
I can change it to maybe 0?
dysgu run \
-p ${cpus} \
-x \
--min-support 0
${fasta} \
. \
${input_bam} \
| bgzip ${args2} --threads ${cpus} --stdout > ${prefix}.vcf.gz
tabix ${args3} ${prefix}.vcf.gz
May I ask for running .cram files I need to add a specific parameters?
There a no additional parameters to use a cram file. Min-support 0 or 1 will have the same effect, i.e. at least one bit of evidence for a SV call
I have tried both 0 and 1 parameters and still there is no change in results, I suppose there's no SV present in the test_data :(
Hi @kcleal Could please suggest me some ideas how to modify the command line to solve this directory errors!
cmd line:-
Thanks.