samtools error
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Hi, I'm trying to run svim with some ONT data I have by mapping to a reference genome (svim reads --cores 20 --nanopore my_sample /media/anthonybarley/extradrive1/mergedtigris.fastq.gz a_marmoratus_AspMarm2.0.fasta). However, I am getting an error, that seems like it might be related to use of samtools within the pipeline. Do you know what the issue and/or fix might be? Standard output is here:
2024-04-22 15:25:12,073 [INFO ] ****************** Start SVIM, version 1.4.2 ******************
2024-04-22 15:25:12,074 [INFO ] CMD: python3 /home/anthonybarley/miniconda3/envs/svim_env/bin/svim reads --cores 20 --nanopore my_sample /media/anthonybarley/extradrive1/mergedtigris.fastq.gz a_marmoratus_AspMarm2.0.fasta
2024-04-22 15:25:12,074 [INFO ] WORKING DIR: /home/anthonybarley/Desktop/whip_genomes/my_sample
2024-04-22 15:25:12,074 [INFO ] PARAMETER: sub, VALUE: reads
2024-04-22 15:25:12,074 [INFO ] PARAMETER: working_dir, VALUE: my_sample
2024-04-22 15:25:12,074 [INFO ] PARAMETER: reads, VALUE: /media/anthonybarley/extradrive1/mergedtigris.fastq.gz
2024-04-22 15:25:12,074 [INFO ] PARAMETER: genome, VALUE: a_marmoratus_AspMarm2.0.fasta
2024-04-22 15:25:12,074 [INFO ] PARAMETER: verbose, VALUE: False
2024-04-22 15:25:12,074 [INFO ] PARAMETER: cores, VALUE: 20
2024-04-22 15:25:12,074 [INFO ] PARAMETER: aligner, VALUE: ngmlr
2024-04-22 15:25:12,074 [INFO ] PARAMETER: nanopore, VALUE: True
2024-04-22 15:25:12,074 [INFO ] PARAMETER: min_mapq, VALUE: 20
2024-04-22 15:25:12,074 [INFO ] PARAMETER: min_sv_size, VALUE: 40
2024-04-22 15:25:12,074 [INFO ] PARAMETER: max_sv_size, VALUE: 100000
2024-04-22 15:25:12,074 [INFO ] PARAMETER: segment_gap_tolerance, VALUE: 10
2024-04-22 15:25:12,074 [INFO ] PARAMETER: segment_overlap_tolerance, VALUE: 5
2024-04-22 15:25:12,074 [INFO ] PARAMETER: all_bnds, VALUE: False
2024-04-22 15:25:12,074 [INFO ] PARAMETER: partition_max_distance, VALUE: 1000
2024-04-22 15:25:12,074 [INFO ] PARAMETER: distance_normalizer, VALUE: 900
2024-04-22 15:25:12,074 [INFO ] PARAMETER: cluster_max_distance, VALUE: 0.3
2024-04-22 15:25:12,074 [INFO ] PARAMETER: del_ins_dup_max_distance, VALUE: 1.0
2024-04-22 15:25:12,074 [INFO ] PARAMETER: trans_sv_max_distance, VALUE: 500
2024-04-22 15:25:12,074 [INFO ] PARAMETER: skip_genotyping, VALUE: False
2024-04-22 15:25:12,074 [INFO ] PARAMETER: minimum_score, VALUE: 3
2024-04-22 15:25:12,074 [INFO ] PARAMETER: homozygous_threshold, VALUE: 0.8
2024-04-22 15:25:12,075 [INFO ] PARAMETER: heterozygous_threshold, VALUE: 0.2
2024-04-22 15:25:12,075 [INFO ] PARAMETER: minimum_depth, VALUE: 4
2024-04-22 15:25:12,075 [INFO ] PARAMETER: sample, VALUE: Sample
2024-04-22 15:25:12,075 [INFO ] PARAMETER: types, VALUE: DEL,INS,INV,DUP:TANDEM,DUP:INT,BND
2024-04-22 15:25:12,075 [INFO ] PARAMETER: sequence_alleles, VALUE: False
2024-04-22 15:25:12,075 [INFO ] PARAMETER: insertion_sequences, VALUE: False
2024-04-22 15:25:12,075 [INFO ] PARAMETER: tandem_duplications_as_insertions, VALUE: False
2024-04-22 15:25:12,075 [INFO ] PARAMETER: interspersed_duplications_as_insertions, VALUE: False
2024-04-22 15:25:12,075 [INFO ] PARAMETER: read_names, VALUE: False
2024-04-22 15:25:12,075 [INFO ] PARAMETER: zmws, VALUE: False
2024-04-22 15:25:12,075 [INFO ] ****************** STEP 1: COLLECT ******************
2024-04-22 15:25:12,075 [INFO ] MODE: reads
2024-04-22 15:25:12,075 [INFO ] INPUT: /media/anthonybarley/extradrive1/mergedtigris.fastq.gz
2024-04-22 15:25:12,075 [INFO ] GENOME: /home/anthonybarley/Desktop/whip_genomes/a_marmoratus_AspMarm2.0.fasta
2024-04-22 15:25:12,075 [INFO ] Recognized reads file as gzipped FASTQ format.
2024-04-22 15:25:12,104 [INFO ] Starting alignment pipeline..
ngmlr 0.2.7 (build: May 16 2023 08:30:10, start: 2024-04-22.15:25:12)
Contact: philipp.rescheneder@univie.ac.at
Writing output (SAM) to stdout
Reading encoded reference from a_marmoratus_AspMarm2.0.fasta-enc.2.ngm
Reading 1643 Mbp from disk took 0.51s
Reading reference index from a_marmoratus_AspMarm2.0.fasta-ht-13-2.2.ngm
Reading from disk took 1.35s
Opening query file /dev/stdin
Mapping reads...
Waiting for data from stdin
Processed: 5605 (0.91), R/S: 140.11, RL: 6001, Time: 5.78 1.05 87.94, Align: 0.97, 561, 0.93
Processed: 5677 (0.91), R/S: 135.15, RL: 6061, Time: 5.67 1.56 85.83, Align: 0.97, 565, 0.93
samtools view: error closing "-": -5
2024-04-22 15:25:58,857 [ERROR ] The alignment pipeline failed with exit code 1. Command was: set -o pipefail && gunzip -c /media/anthonybarley/extradrive1/mergedtigris.fastq.gz | ngmlr -t 20 -r a_marmoratus_AspMarm2.0.fasta -x ont | samtools view -b -@ 20 | samtools sort -@ 20 -o my_sample/mergedtigris.fastq.ngmlr.coordsorted.bam
Traceback (most recent call last):
File "/home/anthonybarley/miniconda3/envs/svim_env/lib/python3.8/site-packages/svim/SVIM_alignment.py", line 52, in run_alignment
run(" ".join(command_align), shell=True, check=True, executable='/bin/bash')
File "/home/anthonybarley/miniconda3/envs/svim_env/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'set -o pipefail && gunzip -c /media/anthonybarley/extradrive1/mergedtigris.fastq.gz | ngmlr -t 20 -r a_marmoratus_AspMarm2.0.fasta -x ont | samtools view -b -@ 20 | samtools sort -@ 20 -o my_sample/mergedtigris.fastq.ngmlr.coordsorted.bam' returned non-zero exit status 1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/anthonybarley/miniconda3/envs/svim_env/bin/svim", line 216, in
sys.exit(main())
File "/home/anthonybarley/miniconda3/envs/svim_env/bin/svim", line 85, in main
bam_path = run_alignment(options.working_dir, options.genome, options.reads, reads_type, options.cores, options.aligner, options.nanopore)
File "/home/anthonybarley/miniconda3/envs/svim_env/lib/python3.8/site-packages/svim/SVIM_alignment.py", line 55, in run_alignment
raise AlignmentPipelineError('The alignment pipeline failed with exit code {0}. Command was: {1}'.format(e.returncode, e.cmd)) from e
svim.SVIM_alignment.AlignmentPipelineError: The alignment pipeline failed with exit code 1. Command was: set -o pipefail && gunzip -c /media/anthonybarley/extradrive1/mergedtigris.fastq.gz | ngmlr -t 20 -r a_marmoratus_AspMarm2.0.fasta -x ont | samtools view -b -@ 20 | samtools sort -@ 20 -o my_sample/mergedtigris.fastq.ngmlr.coordsorted.bam
Thanks!