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eldariont
samtools error
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: [email protected] 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
Thanks!
