Crash when providing SRR list

[anearman]

Hello! I am receiving the following error when providing a list of short read archives.

ERROR ~ Error executing process > 'egapx:rnaseq_short_plane:fetch_sra_fasta:run_fetch_sra_fasta (2)'

Caused by:
Process egapx:rnaseq_short_plane:fetch_sra_fasta:run_fetch_sra_fasta (2) terminated with an error exit status (1)

Command executed:

output_SRR035924=$(srapath SRR035924)
curl -o SRR035924 $output_SRR035924
fasterq-dump --skip-technical --threads 6 --split-files --seq-defline ">$ac.$si.$ri" --fasta -O . ./SRR035924
rm -f SRR035924
mkdir output
mv SRR035924_1.fasta output/SRR035924.1
if [ -f SRR035924_2.fasta ]; then
mv SRR035924_2.fasta output/SRR035924.2
fi

Command exit status:
1

Command output:
(empty)

Command error:
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
1 1464M 1 15.3M 0 0 12.5M 0 0:01:57 0:00:01 0:01:56 12.4M
3 1464M 3 53.7M 0 0 24.1M 0 0:01:00 0:00:02 0:00:58 24.1M
6 1464M 6 92.2M 0 0 28.6M 0 0:00:51 0:00:03 0:00:48 28.5M
8 1464M 8 130M 0 0 30.8M 0 0:00:47 0:00:04 0:00:43 30.8M
11 1464M 11 163M 0 0 31.2M 0 0:00:46 0:00:05 0:00:41 32.8M
13 1464M 13 199M 0 0 32.0M 0 0:00:45 0:00:06 0:00:39 36.8M
15 1464M 15 232M 0 0 32.1M 0 0:00:45 0:00:07 0:00:38 35.6M
18 1464M 18 271M 0 0 33.0M 0 0:00:44 0:00:08 0:00:36 35.8M
20 1464M 20 304M 0 0 32.8M 0 0:00:44 0:00:09 0:00:35 34.4M
23 1464M 23 348M 0 0 34.0M 0 0:00:43 0:00:10 0:00:33 36.9M
26 1464M 26 391M 0 0 34.8M 0 0:00:42 0:00:11 0:00:31 38.3M
29 1464M 29 424M 0 0 34.7M 0 0:00:42 0:00:12 0:00:30 38.5M
30 1464M 30 451M 0 0 34.1M 0 0:00:42 0:00:13 0:00:29 35.9M
32 1464M 32 481M 0 0 33.8M 0 0:00:43 0:00:14 0:00:29 35.6M
35 1464M 35 517M 0 0 33.9M 0 0:00:43 0:00:15 0:00:28 33.7M
37 1464M 37 553M 0 0 34.1M 0 0:00:42 0:00:16 0:00:26 32.4M
40 1464M 40 589M 0 0 34.1M 0 0:00:42 0:00:17 0:00:25 32.7M
42 1464M 42 625M 0 0 34.2M 0 0:00:42 0:00:18 0:00:24 34.7M
45 1464M 45 664M 0 0 34.5M 0 0:00:42 0:00:19 0:00:23 36.6M
48 1464M 48 705M 0 0 34.8M 0 0:00:42 0:00:20 0:00:22 37.6M
50 1464M 50 741M 0 0 34.9M 0 0:00:41 0:00:21 0:00:20 37.4M
53 1464M 53 778M 0 0 35.0M 0 0:00:41 0:00:22 0:00:19 38.0M
55 1464M 55 816M 0 0 35.0M 0 0:00:41 0:00:23 0:00:18 37.7M
57 1464M 57 835M 0 0 34.4M 0 0:00:42 0:00:24 0:00:18 34.2M
59 1464M 59 868M 0 0 34.4M 0 0:00:42 0:00:25 0:00:17 32.7M
61 1464M 61 896M 0 0 34.1M 0 0:00:42 0:00:26 0:00:16 31.0M
63 1464M 63 926M 0 0 34.0M 0 0:00:43 0:00:27 0:00:16 29.5M
65 1464M 65 959M 0 0 33.9M 0 0:00:43 0:00:28 0:00:15 29.0M
67 1464M 67 994M 0 0 34.0M 0 0:00:43 0:00:29 0:00:14 31.7M
70 1464M 70 1027M 0 0 34.0M 0 0:00:43 0:00:30 0:00:13 31.8M
73 1464M 73 1071M 0 0 34.3M 0 0:00:42 0:00:31 0:00:11 35.0M
75 1464M 75 1111M 0 0 34.4M 0 0:00:42 0:00:32 0:00:10 37.1M
78 1464M 78 1144M 0 0 34.4M 0 0:00:42 0:00:33 0:00:09 36.9M
80 1464M 80 1184M 0 0 34.4M 0 0:00:42 0:00:34 0:00:08 37.0M
83 1464M 83 1219M 0 0 34.6M 0 0:00:42 0:00:35 0:00:07 38.1M
85 1464M 85 1248M 0 0 34.4M 0 0:00:42 0:00:36 0:00:06 35.3M
87 1464M 87 1283M 0 0 34.4M 0 0:00:42 0:00:37 0:00:05 34.4M
89 1464M 89 1315M 0 0 34.4M 0 0:00:42 0:00:38 0:00:04 34.2M
92 1464M 92 1360M 0 0 34.6M 0 0:00:42 0:00:39 0:00:03 36.2M
95 1464M 95 1399M 0 0 34.7M 0 0:00:42 0:00:40 0:00:02 36.1M
97 1464M 97 1430M 0 0 34.6M 0 0:00:42 0:00:41 0:00:01 36.3M
99 1464M 99 1456M 0 0 34.4M 0 0:00:42 0:00:42 --:--:-- 34.4M
100 1464M 100 1464M 0 0 34.3M 0 0:00:42 0:00:42 --:--:-- 34.2M
spots read : 1,263,141
reads read : 2,526,282
reads written : 1,263,141
technical reads : 1,263,141
mv: cannot stat 'SRR035924_1.fasta': No such file or directory

[pstrope]

Hi,
Thank you for reporting this issue. This was some unexpected format in the SRR data. We will add a check for such formats. It will be released in the next version.

Pooja