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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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Confused with the last version releases #79

Open Manuel-DominguezCBG opened 4 months ago

Manuel-DominguezCBG commented 4 months ago

In our clinical lab, the previous bioinformatician installed Pisces 5.2.11.163. I have also seen this version in issues submitted by other people. However, I am not able to find that release. Where is this? or what is the most equivalent??

tamsen commented 4 months ago

Hi there,

Since 5.2.11.163 is not one of the releases on github, you might want to contact illumina tech support if you have questions about that specific release. If you have errors, I'd suggest rolling over to v5.3.0.0 from https://github.com/tamsen/Pisces , which has been more recently maintained.

Thanks for using Pisces :-)

Tamsen

Manuel-DominguezCBG commented 4 months ago

Version 5.3.0.0 is a prerelease. Can I use it with the same level of confidence as version 5.2.10?

I have an important question for which I would appreciate your advice.

Does MultiGemini work with single-read data? After reviewing the results, I get the impression that when single-read BAM files are processed, no indel realignment is performed. Is this correct?

No errors or warnings are reported in the different log files. Indels tables (FinalIndels.csv, IndelOutcomes.csv, _Indels.csv and CategoryOutcomes.csv) are empty. The GeminiLog files looks all like this.

2/9/2024 2:40 AM 1  ************* Starting **************
2/9/2024 2:40 AM 1  Version:  5.2.11.163.
2/9/2024 2:40 AM 1  Command-line arguments: .
2/9/2024 2:40 AM 1  "--samtools D:\WRGLPipeline-local\Samtools\1.3.1\samtools.exe --genome D:\WRGLPipeline-local\data\human_g1k_v37 --bam F:\Illumina\MiSeqOutput\240207_M00321_0131_000000000-LCWP3\Data\Intensities\Basecalls\\Genotyping_2.22\436260858_sorted.bam --chromRefId 0 --outFolder F:\Illumina\MiSeqOutput\240207_M00321_0131_000000000-LCWP3\Data\Intensities\Basecalls\\Genotyping_2.22\436260858\1".
2/9/2024 2:40 AM 1  At 0, prev block is -1, nothing to wait on.
2/9/2024 2:40 AM 1  At 0:43814950. Processed 0 reads and 0 pairs so far. 0 skipped, 0 skipped and blacklisted, 0 pairs skipped, 0 pairs paired, 0 currently waiting for mate. Blacklist: 0.
2/9/2024 2:40 AM 4  Finished processing for region 1:0-10000000. 0 alignments flushed, 0 sent to next block, 0 retrieved from . Realigned 0/0 attempts (0 pairs skipped realignment), silenced 0 messy mates.
2/9/2024 2:40 AM 1  Borderline pairs left: 0.
2/9/2024 2:40 AM 1  Wrote 0 reads with missing mates to bam.
2/9/2024 2:40 AM 1  Triggering last buffer batch. Read 3 read pairs. Flushed 0 singles.
2/9/2024 2:40 AM 1  Completing buffer.
2/9/2024 2:40 AM 1  Now waiting on 5 tasks.
2/9/2024 2:40 AM 6  Finished processing for region 1:10000001-53814950. 0 alignments flushed, 0 sent to next block, 0 retrieved from 0-10000000. Realigned 0/0 attempts (0 pairs skipped realignment), silenced 0 messy mates.
2/9/2024 2:40 AM 8  Finished processing for region 1:53814951-63814950. 0 alignments flushed, 0 sent to next block, 0 retrieved from 10000001-53814950. Realigned 0/0 attempts (0 pairs skipped realignment), silenced 0 messy mates.
2/9/2024 2:40 AM 1  Done waiting on tasks.
2/9/2024 2:40 AM 1  Found 0 total indels, and 0 eligible for realignment.
2/9/2024 2:40 AM 1  Attempts: 0.
2/9/2024 2:40 AM 1  Early Flushed: 3.
2/9/2024 2:40 AM 1  Flushed: 0.
2/9/2024 2:40 AM 1  Realigned: 0.
2/9/2024 2:40 AM 1  Retrieved from Past Block: 0.
2/9/2024 2:40 AM 1  Sent To Next Block: 0.
2/9/2024 2:40 AM 1  Silenced: 0.
2/9/2024 2:40 AM 1  Simple Alignments Written: 3.
2/9/2024 2:40 AM 1  Skipped: 0.
2/9/2024 2:40 AM 1  CATEGORY Improper: 3.
2/9/2024 2:40 AM 1  Calling cat on 1 with output at F:\Illumina\MiSeqOutput\240207_M00321_0131_000000000-LCWP3\Data\Intensities\Basecalls\\Genotyping_2.22\436260858\1\merged.bam.
2/9/2024 2:40 AM 1  Intermediate bam: F:\Illumina\MiSeqOutput\240207_M00321_0131_000000000-LCWP3\Data\Intensities\Basecalls\\Genotyping_2.22\436260858\1\out.bam_0_1_All_All_0_1_All_All_7_7_0_c3025d28-2a04-43dc-ac67-aef067ff39e9 2100B.
2/9/2024 2:40 AM 1  Skipping samtools cat due to single input bam, instead moving F:\Illumina\MiSeqOutput\240207_M00321_0131_000000000-LCWP3\Data\Intensities\Basecalls\\Genotyping_2.22\436260858\1\out.bam_0_1_All_All_0_1_All_All_7_7_0_c3025d28-2a04-43dc-ac67-aef067ff39e9 directly to output at F:\Illumina\MiSeqOutput\240207_M00321_0131_000000000-LCWP3\Data\Intensities\Basecalls\\Genotyping_2.22\436260858\1\merged.bam.
2/9/2024 2:40 AM 1  Calling samtools sort on F:\Illumina\MiSeqOutput\240207_M00321_0131_000000000-LCWP3\Data\Intensities\Basecalls\\Genotyping_2.22\436260858\1\merged.bam.
2/9/2024 2:40 AM 1  Done finalizing bam.
2/9/2024 2:40 AM 1  Deleting intermediate bams.
2/9/2024 2:40 AM 1  Finished deleting intermediate bams.
2/9/2024 2:40 AM 1  ******************** Ending *********************

Thank you again for your help

Manuel-DominguezCBG commented 4 months ago

I have found this

image

I think that this information should be in the README file.

I think that a safer program should stop the analysis/execution and not hide the error.