Cannot find temporary files

[devmon]

So the program creates temporary files in /tmp/pfd_0hm17d1p but at the end, it cannot find the second fastq file: FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pfd_0hm17d1p/10/SRR4253583_2.fastq'

$ parallel-fastq-dump --sra-id SRR4253583 -t 16 -O out/ --split-files SRR ids: ['SRR4253583'] extra args: ['--split-files'] SRR4253583 spots: 143228176 tempdir: /tmp/pfd_0hm17d1p blocks: [[1, 8951761], [8951762, 17903522], [17903523, 26855283], [26855284, 35807044], [35807045, 44758805], [44758806, 53710566], [53710567, 62662327], [62662328, 71614088], [71614089, 80565849], [80565850, 89517610], [89517611, 98469371], [98469372, 107421132], [107421133, 116372893], [116372894, 125324654], [125324655, 134276415], [134276416, 143228176]]Rejected 8951761 READS because READLEN < 1 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Rejected 8951761 READS because READLEN < 1 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Rejected 8951761 READS because READLEN < 1 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Rejected 8951761 READS because READLEN < 1 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Rejected 8951761 READS because READLEN < 1 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Rejected 8951761 READS because READLEN < 1 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Rejected 1880687 READS because READLEN < 1 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Read 8951761 spots for SRR4253583 Written 8951761 spots for SRR4253583 Traceback (most recent call last): File "/home/$username/anaconda3/bin/parallel-fastq-dump", line 4, in import('pkg_resources').run_script('parallel-fastq-dump==0.6.2', 'parallel-fastq-dump') File "/home/$username/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 750, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/$username/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 1534, in run_script exec(script_code, namespace, namespace) File "/home/$username/anaconda3/lib/python3.6/site-packages/parallel_fastq_dump-0.6.2-py3.6.egg/EGG-INFO/scripts/parallel-fastq-dump", line 100, in File "/home/$username/anaconda3/lib/python3.6/site-packages/parallel_fastq_dump-0.6.2-py3.6.egg/EGG-INFO/scripts/parallel-fastq-dump", line 93, in main File "/home/$username/anaconda3/lib/python3.6/site-packages/parallel_fastq_dump-0.6.2-py3.6.egg/EGG-INFO/scripts/parallel-fastq-dump", line 43, in pfd FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pfd_0hm17d1p/10/SRR4253583_2.fastq'

Thanks!

[rvalieris]

hello,

looks like, in this specific run, there are many reads being filtered out (Rejected 1880687 READS because READLEN < 1), and because of that not all blocks have both files _1 and _2.

I will investigate this SRR and see what we can do.

[devmon]

It works with normal fastq-dump.

[rvalieris]

so, I was assuming all blocks of a SRR would have the same files, but in cases like this were lots of reads were filtered this is not true, in 0.6.3 I only merge the files present in each block.

[rvalieris]

0.6.3 is out with the fix

[devmon]

Thank you again!