Hi, I am running the presplit_map.py script on a SLURM cluster on a small dataset (MboI restriction enzyme used).
here's the command I am running:
python presplit_map.py -G ~/../Bowtie2Index/hg19 -1 ~/../fastq/HIC003_R1.fastq.gz -2 ~/../fastq/HIC003_R2.fastq.gz --sig GATCGATC -o HIC003.bam
I am using python-2.7.10, cutadapt-1.8.3 and bowtie2/2.2.4 versions
Once the script starts running, a temporary folder is generated and a HIC003_R1.fastq.bam file is created, after which the job fails and gives me the following error:
[E::hts_open] fail to open file './tmpnA4PdG/sorted.bam'
Traceback (most recent call last):
File "presplit_map.py", line 242, in <module>
pysam.sort("-o", bsorted, "-n", outbam)
File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/pysam/__init__.py", line 79, in __call__
(retval, "\n".join(stderr)))
pysam.SamtoolsError: 'csamtools returned with error 1: [bam_sort_core] fail to open file ./tmpnA4PdG/sorted.bam\n'
I tried googling this error message and did not find any good solutions. Any idea what may be going wrong in this case?
thanks, - Iftekhar
Hi Aaron,
The Bam file HIC003_R1.fastq.bam looks ok:
M00336:181:000000000-A29H6:1:1101:17139:1645 2129 chr17 62341747 42 80M20H * 0 0 HGFHHGCFDAGBHGG2HGFHHHFFHFHGFACGGFFDGGHHHHHHHGHHFGG AS:i:-8 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:0A50C2 M00336:181:000000000-A29H6:1:1101:14932:1669 81 chr1 245889622 42 8H92M * 0 0 11E?1GFHGBEGHBHHHGHHEGGGGGFCHGHGECEGHEGHF2HGHFHHHGEGGGGGGGGFFFFFFF>ABAA AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM: M00336:181:000000000-A29H6:1:1101:14932:1669 2129 chr20 683971 1 8M92H * 0 0 CAC M00336:181:000000000-A29H6:1:1101:14615:1679 81 chr7 17169791 42 38H62M * 0 0 A@DBA?AA3 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:62 YT:Z:UU M00336:181:000000000-A29H6:1:1101:14615:1679 2129 chr7 17176069 42 38M62H * 0 0 0 NM:i:0 MD:Z:38 YT:Z:UU M00336:181:000000000-A29H6:1:1101:13929:1684 81 chr20 11892330 42 63H37M * 0 0 0 NM:i:0 MD:Z:37 YT:Z:UU M00336:181:000000000-A29H6:1:1101:13929:1684 2113 chr6 51812440 42 37H63M * 0 0 G>BGGGHHGH AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:63 YT:Z:UU M00336:181:000000000-A29H6:1:1101:15728:1726 65 chr6 90191921 42 70M30H * 0 0 FGFFFGBF1GFHBFFH/BEABEEGC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YT:Z:UU
I ran the following script on the Python interpreter:
import os import pysam tmpdir="tmpnA4PdG" outbam=os.path.join(tmpdir, "HIC003_R1.fastq.bam") bsorted=os.path.join(tmpdir, "sorted.bam") pysam.sort("-o", bsorted, "-n", outbam)
And ended up getting a similar error message as before:
[E::htsopen] fail to open file 'tmpnA4PdG/sorted.bam' Traceback (most recent call last): File "pysamtroubleshoot.py", line 6, in <module> pysam.sort("-o", bsorted, "-n", outbam) File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/pysam/init.py", line 79, in call (retval, "\n".join(stderr))) pysam.SamtoolsError: 'csamtools returned with error 1: [bamsortcore] fail to open file tmpnA4PdG/sorted.bam\n'
I am using pysam 0.8.4 with python-2.7.10 in our cluster. I also tried using python-3.6.5 which comes with pysam 0.15.1, but it gives me a different error message and no bam files are created in this case:
Traceback (most recent call last): File "presplitmap.py", line 116, in <module> raise SystemError("cutadapt failed to trim reads\n"+cuterr) TypeError: must be str, not bytes
I ended up switching the cutadapt version from cutadapt-1.8.3 to cutadapt-2.3 and it looks like that solved the issue.
thank you, - Iftekhar