search

ncbi / sra-tools

SRA Tools
Other
1.12k stars 246 forks source link

fasterq-dump failure on multiple accessions (all PacBio runs in this case) #440

Closed seandavi closed 3 years ago

seandavi commented 3 years ago 
for i in SRR5219188 SRR5219189 SRR9599028 SRR9599029 SRR9599030 SRR9599031 SRR9599032 SRR9599033 SRR9599034 SRR9599035 SRR9599036 SRR9599037 SRR9599038 SRR9599039 SRR9599040 SRR9599041 SRR9599042 SRR9599043 SRR9599044 SRR9599045 SRR9599046 SRR9599047 SRR9599048 SRR9599049 SRR9599050 SRR9599051 SRR9599052 SRR9599053 SRR9599054 SRR9599055 SRR9599056 SRR9599057 SRR9599058 SRR9599059 SRR9599060 SRR9599061 SRR9599062 SRR9599063 SRR9599064 SRR9599065 SRR9599066 SRR9599067 SRR9599068 SRR9599069 SRR9599070 SRR9599071 SRR9599072 SRR9599073 SRR9599074 SRR9599075 SRR9599076 SRR9599077 SRR9599177; do echo $i; fasterq-dump           --skip-technical           --force           --threads 1           --split-files $i; done

Results in:

SRR5219188
2020-11-23T01:34:41 fasterq-dump.2.10.8 err: row#4 : bits=32, boff=0, len=0
2020-11-23T01:34:43 fasterq-dump.2.10.8 err: row#91332 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR5219189
2020-11-23T01:34:50 fasterq-dump.2.10.8 err: row#81848 : bits=32, boff=0, len=0
2020-11-23T01:34:50 fasterq-dump.2.10.8 err: row#1114 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599028
2020-11-23T01:35:02 fasterq-dump.2.10.8 err: row#14878 : bits=32, boff=0, len=0
2020-11-23T01:35:14 fasterq-dump.2.10.8 err: row#131727 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599029
2020-11-23T01:35:32 fasterq-dump.2.10.8 err: row#1853 : bits=32, boff=0, len=0
2020-11-23T01:35:34 fasterq-dump.2.10.8 err: row#90938 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599030
2020-11-23T01:35:45 fasterq-dump.2.10.8 err: row#83764 : bits=32, boff=0, len=0
2020-11-23T01:35:48 fasterq-dump.2.10.8 err: row#12419 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599031
2020-11-23T01:35:55 fasterq-dump.2.10.8 err: row#82568 : bits=32, boff=0, len=0
2020-11-23T01:35:58 fasterq-dump.2.10.8 err: row#11805 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599032
2020-11-23T01:36:08 fasterq-dump.2.10.8 err: row#3930 : bits=32, boff=0, len=0
2020-11-23T01:36:09 fasterq-dump.2.10.8 err: row#87795 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599033
2020-11-23T01:36:18 fasterq-dump.2.10.8 err: row#88650 : bits=32, boff=0, len=0
2020-11-23T01:36:21 fasterq-dump.2.10.8 err: row#21866 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599034
2020-11-23T01:36:34 fasterq-dump.2.10.8 err: row#107479 : bits=32, boff=0, len=0
2020-11-23T01:36:34 fasterq-dump.2.10.8 err: row#32507 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599035
2020-11-23T01:36:44 fasterq-dump.2.10.8 err: row#5544 : bits=32, boff=0, len=0
2020-11-23T01:36:47 fasterq-dump.2.10.8 err: row#94437 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599036
2020-11-23T01:37:00 fasterq-dump.2.10.8 err: row#12634 : bits=32, boff=0, len=0
2020-11-23T01:37:04 fasterq-dump.2.10.8 err: row#104728 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599037
2020-11-23T01:37:24 fasterq-dump.2.10.8 err: row#16643 : bits=32, boff=0, len=0
2020-11-23T01:37:46 fasterq-dump.2.10.8 err: row#161973 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3
SRR9599038
2020-11-23T01:38:07 fasterq-dump.2.10.8 err: row#12634 : bits=32, boff=0, len=0
2020-11-23T01:38:40 fasterq-dump.2.10.8 err: row#140044 : bits=32, boff=0, len=0
fasterq-dump quit with error code 3

These all look to be PacBio runs, so I suspect there is a systematic issue here somewhere. Any suggestions?

seandavi commented 3 years ago

This looks related to: https://github.com/ncbi/sra-tools/issues/318#issuecomment-661121843

If the expected fix is to not use fasterq-dump with PacBio runs loaded with pacbio-load, is there not a way to fall back to fastq-dump when this error arises rather than requiring the user to catch the error by hand (note that there is no way to computationally catch this error, specifically) and then troubleshoot?

klymenko commented 3 years ago

Now fasterq-dump SRR5219188 prints the following message: 2020-12-18T20:11:06 fasterq-dump.2.10.9 err: accession 'SRR5219188' is PACBIO, please use fastq-dump instead

Unfortunately fasterq-dump does not support PacBio runs. Use fastq-dump instead.

JonEilers commented 1 year ago

I am trying to unpack some pacbio SRA files using fastq-dump 3.0.1 and it throws this error

fastq-dump SRR10130136.sra
2023-02-14T20:46:42 fastq-dump.3.0.1 err: accession 'SRR10130136' is PACBIO, please use fastq-dump instead