Run errors
gevro opened this issue · 2 comments
Hi, I'm running into trouble and getting several errors:
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I'm using the latest 1.1.1 version.
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Input is a BAM file with config:
#sample_name bam vcf depth sex
60603-W1-B2 60603-W1-B2.cram 60603-W1-B2.filtered.vcf.gz 51.3408 M -
input.log shows this:
ANNOVAR Version:
$Date: 2020-06-07 23:56:37 -0400 (Sun, 7 Jun 2020) $
ANNOVAR Information:
For questions, comments, documentation, bug reports and program update, please visit http://www.openbioinformatics.org/annovar/
ANNOVAR Command:
/bin/annovar/annotate_variation.pl -filter -build hg38 -dbtype gnomad_genome /tmp/tmpy7mejtlt /bin/annovar/humandb -outfile 60603-W1-B2/input
ANNOVAR Started:
Fri Aug 25 18:38:21 2023
NOTICE: Output file with variants matching filtering criteria is written to 60603-W1-B2/input.hg38_gnomad_genome_dropped, and output file with other variants is written to 60603-W1-B2/input.hg38_gnomad_genome_filtered
NOTICE: Processing next batch with 3158595 unique variants in 3158595 input lines
NOTICE: Database index loaded. Total number of bins is 28084439 and the number of bins to be scanned is 2768371
NOTICE: Scanning filter database /bin/annovar/humandb/hg38_gnomad_genome.txt...Done
- Output:
- input.hg38_gnomad_genome_filtered has 201,820 lines
- features.txt is empty
- images and matrices folders are empty
- In STDERR, I'm getting this WARNING when I run deepmosaic-draw:
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "C.UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
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After this step: "NOTICE: Scanning filter database /bin/annovar/humandb/hg38_gnomad_genome.txt...Done
/DeepMosaic/deepmosaic/gnomadAnnotation.py:30: DtypeWarning: Columns (1) have mixed types. Specify dtype option on import or set low_memory=False.
df = pd.read_csv(output_dir + "input." + build + "_" + dbtype + "_dropped", header=None, sep="\t")"I'm getting a bunch of these warnings (thousands of lines) right when the pipeline starts:
/reference-files/cram-cache/6a/ef/897c3d6ff0c78aff06ac189178dd.tmp_260008_1_2600980418: No such file or directory
/reference-files/cram-cache/6a/ef/897c3d6ff0c78aff06ac189178dd.tmp_260007_1_2601222400: No such file or directory
/reference-files/cram-cache/6a/ef/897c3d6ff0c78aff06ac189178dd.tmp_260012_1_2601368861: No such file or directory
/reference-files/cram-cache/6a/ef/897c3d6ff0c78aff06ac189178dd.tmp_260011_1_2601476278: No such file or directory
/reference-files/cram-cache/6a/ef/897c3d6ff0c78aff06ac189178dd.tmp_260010_1_2600633160: No such file or directory
/reference-files/cram-cache/6a/ef/897c3d6ff0c78aff06ac189178dd.tmp_260006_1_2601420330: No such file or directory
[E::cram_read_container] Container header CRC32 failure
It looks like there are CRAM warnings/errors, but there is no CRAM input into the pipeline. So I'm not sure what the issue is.
Can you please assist?
Thanks!
You're right - sorry I missed that bug! Even though I converted to BAM, I was still putting CRAM in the config.