skesa failed with code -9

[mabouelk]

I got this error when I ran RAPT on paired end illumina fastq files.

**Error: skesa failed with code -9
[2022-07-08 20:56:34] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-04-14.build6021&uuid=3b0d8616-ff00-11ec-810c-501fc65b9c25&evt=skesa_failed&rcode=-9
[2022-07-08 20:56:34] Usage metrics sent to NCBI
[2022-07-08 20:56:36] Download blob input-2022-04-14.build6021.prod.ani.tgz aborted
[2022-07-08 20:56:37] Download blob input-2022-04-14.build6021.prod.tgz aborted
[2022-07-08 20:56:37] status=5
[2022-07-08 20:56:37] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-04-14.build6021&uuid=3b0d8616-ff00-11ec-810c-501fc65b9c25&evt=rapt_exit
[2022-07-08 20:56:37] Usage metrics sent to NCBI

[thibaudnis]

I am sorry you are experiencing issues. What are the two lines just prior to "Error: skesa failed with code -9"?
If you are willing to share the files you used, I'd be happy to try to reproduce the error. You could post them somewhere I can access them such as a Cloud bucket or Google Drive and send me the details at prokaryote-tools@ncbi.nlm.nih.gov. Thank you for reporting the error!

[mabouelk]

I re ran it again but I got another error

[2022-07-14 13:15:57] WARNING Final process status is permanentFail

[2022-07-14 13:16:41] Pipeline taxcheck failed with code 1.
[2022-07-14 13:16:41] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-04-14.build6021&uuid=49ee803e-0376-11ed-9e5c-501fc65b9c25&evt=ani_failed&rcode=1
[2022-07-14 13:16:41] Usage metrics sent to NCBI
[2022-07-14 13:16:41] status=18
[2022-07-14 13:16:41] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-04-14.build6021&uuid=49ee803e-0376-11ed-9e5c-501fc65b9c25&evt=rapt_exit
[2022-07-14 13:16:41] Usage metrics sent to NCBI

[thibaudnis]

Is the file ani-tax-report.txt in the output directory? Can you please specify the exact command you ran and attach the log file? And again, if you are willing to share the input files, I'd be happy to try to reproduce the error. Thanks!

[mabouelk]

verbose.log
concise.log

This is on the test file SRR3496277.

[thibaudnis]

Thanks for reporting the issue with the SRA input. We have fixed the problem and rolled out a release with a fix for accessing the SRA archive. You can download and untar it with:

curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.3/rapt-v0.5.3.tar.gz
tar -xzf rapt.tar.gz && rm -f rapt.tar.gz

After that, re-execution using an SRA run as input should succeed.
However, I don't think that it will fix the failures that you experienced with the fastq input. What command did you use for running RAPT from the fastq?

[mabouelk]

Thank you for your help

I downloaded the new release but I got the code-9 again

(base) mohamedabouelkhair@MOHAMEDs-MBP ~ % ./run_rapt.py -a srr3496277
RAPT is now running, it may take a long time to finish. To see the progress, track the verbose log file /Users/mohamedabouelkhair/raptout_6bbcbda04b/verbose.log.

2022-07-16T03:56:35 prefetch.2.11.0: 1) Downloading 'SRR3496277'...
2022-07-16T03:56:35 prefetch.2.11.0: Downloading via HTTPS...
2022-07-16T04:00:23 prefetch.2.11.0: HTTPS download succeed
2022-07-16T04:00:39 prefetch.2.11.0: 'SRR3496277' is valid
2022-07-16T04:00:39 prefetch.2.11.0: 1) 'SRR3496277' was downloaded successfully
total 3737600
drwxr-xr-x 3 501 games 96 Jul 16 04:00 SRR3496277
-rw-r--r-- 1 501 games 1609564160 Jul 16 04:00 ani_ref.tgz
-rw-r--r-- 1 501 games 2214592512 Jul 16 04:00 pgap_ref.tgz
-rw-r--r-- 1 501 games 0 Jul 16 04:00 stdcap.bin

[2022-07-16 04:02:43] **Error: skesa failed with code -9
[2022-07-16 04:02:43] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-04-14.build6021&uuid=86bbcbda-04ba-11ed-ad2b-3af9d351a5a1&evt=skesa_failed&rcode=-9
[2022-07-16 04:02:45] Usage metrics sent to NCBI
[2022-07-16 04:02:47] Download blob input-2022-04-14.build6021.prod.tgz aborted
[2022-07-16 04:02:49] Download blob input-2022-04-14.build6021.prod.ani.tgz aborted
[2022-07-16 04:02:49] status=5
[2022-07-16 04:02:50] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-04-14.build6021&uuid=86bbcbda-04ba-11ed-ad2b-3af9d351a5a1&evt=rapt_exit
[2022-07-16 04:02:50] Usage metrics sent to NCBI

[thibaudnis]

We are not able to reproduce this error. How much CPU and memory is available on you machine? Can you please attach the verbose log, /Users/mohamedabouelkhair/raptout_6bbcbda04b/verbose.log?

[BTalamantesBecerra]

Hi, I am having the same error of **Error: skesa failed with code -9 . Was this issue fixed?

here is the verbose log for error 9:

[2023-04-21 06:30:00] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-10-03.build6384&uuid=f01e157c-e00d-11ed-a0f4-00>[2023-04-21 06:30:02] Usage metrics sent to NCBI
[2023-04-21 06:30:02] rapt-41589182

[2023-04-21 06:30:02] Pipeline starting ..
[2023-04-21 06:30:02] Found input: single FASTQ/A file SRR3496277.fastq
[2023-04-21 06:30:02] FASTQ/A data
@SRR3496277.1.1 HISEQ05:357:C2WVHACXX:4:1101:1794: ...
[2023-04-21 06:30:02] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-10-03.build6384&uuid=f01e157c-e00d-11ed-a0f4-00>[2023-04-21 06:30:02] Start to download reference data ...
[2023-04-21 06:30:03] Downloading https://s3.amazonaws.com/pgap/input-2022-10-03.build6384.prod.ani.tgz
[2023-04-21 06:30:03] Downloading https://s3.amazonaws.com/pgap/input-2022-10-03.build6384.prod.tgz
[2023-04-21 06:30:03] Usage metrics sent to NCBI
[2023-04-21 06:30:03] Starting skesa ...
[2023-04-21 06:30:03] Running command skesa --contigs_out /dkm_output_dir/skesa_out.fa --use_paired_ends --reads /dkm_input_dir/SRR3496277.fastq
[2023-04-21 06:30:33] skesa --contigs_out /dkm_output_dir/skesa_out.fa --use_paired_ends --reads /dkm_input_dir/SRR3496277.fastq

[2023-04-21 06:31:04] Total reads: 9608772
Reads acquired in 51.107164s wall, 49.660000s user + 1.430000s system = 51.090000s CPU (100.0%)

Kmer len: 19
Raw kmers: 1268168907 Memory needed (GB): 24.3488 Memory available (GB): 29.5649 1 cycle(s) will be performed

**[2023-04-21 06:31:34] Error: skesa failed with code -9
[2023-04-21 06:31:34] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-10-03.build6384&uuid=f01e157c-e00d-11ed-a0f4-00>[2023-04-21 06:31:36] Usage metrics sent to NCBI
[2023-04-21 06:31:59] Download blob input-2022-10-03.build6384.prod.ani.tgz aborted
[2023-04-21 06:32:09] Download blob input-2022-10-03.build6384.prod.tgz aborted
[2023-04-21 06:32:09] status=5
[2023-04-21 06:32:09] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-10-03.build6384&uuid=f01e157c-e00d-11ed-a0f4-00>[2023-04-21 06:32:10] Usage metrics sent to NCBI

[thibaudnis]

Thanks for reporting the issue. How much CPU and memory is available on you machine? Can you please attach the verbose.log file that should be in the output directory? Thanks!

[wurunbiao162]

Hi，I get a problem but now I do not how to solve it when I run rapt on my docker, the verbose.log file information is as follow. Thanks.

[2023-07-21 01:07:03] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-10-03.build6384&uuid=e4929b00-2762-11ee-b0a3-525400178bd9&evt=rapt_start&
[2023-07-21 01:07:05] Usage metrics sent to NCBI
[2023-07-21 01:07:05] rapt-41589182

[2023-07-21 01:07:05] Pipeline starting ..
[2023-07-21 01:07:06] Found input: single gzipped FASTQ/A file SRR3496277.fastq.gz
[2023-07-21 01:07:06] GZipped FASTQ/A data
@SRR3496277.1.1 HISEQ05:357:C2WVHACXX:4:1101:1794: ...
[2023-07-21 01:07:06] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-10-03.build6384&uuid=e4929b00-2762-11ee-b0a3-525400178bd9&evt=skesa_start&input_type=fastq
[2023-07-21 01:07:06] Start to download reference data ...
[2023-07-21 01:07:07] Usage metrics sent to NCBI
[2023-07-21 01:07:07] Starting skesa ...
[2023-07-21 01:07:07] Running command skesa --contigs_out /dkm_output_dir/skesa_out.fa --use_paired_ends --reads /dkm_input_dir/SRR3496277.fastq.gz
[2023-07-21 01:07:09] Downloading https://s3.amazonaws.com/pgap/input-2022-10-03.build6384.prod.ani.tgz
[2023-07-21 01:07:09] Downloading https://s3.amazonaws.com/pgap/input-2022-10-03.build6384.prod.tgz
[2023-07-21 01:07:39] skesa --contigs_out /dkm_output_dir/skesa_out.fa --use_paired_ends --reads /dkm_input_dir/SRR3496277.fastq.gz

[2023-07-21 01:09:39] **Error: skesa failed with code -9
[2023-07-21 01:09:39] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-10-03.build6384&uuid=e4929b00-2762-11ee-b0a3-525400178bd9&evt=skesa_failed&rcode=-9
[2023-07-21 01:09:40] Usage metrics sent to NCBI
[2023-07-21 01:11:06] Download blob input-2022-10-03.build6384.prod.ani.tgz aborted
[2023-07-21 01:21:11] Download blob input-2022-10-03.build6384.prod.tgz aborted
[2023-07-21 01:21:11] status=5
[2023-07-21 01:21:11] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2022-10-03.build6384&uuid=e4929b00-2762-11ee-b0a3-525400178bd9&evt=rapt_exit
[2023-07-21 01:21:12] Usage metrics sent to NCBI

[thibaudnis]

Thanks for reporting the issue. How much CPU and memory is available on you machine?

[wurunbiao162]

[techshine2018]

@wurunbiao162 Looks like your machine have very low memory. please see the minimal requirements here to run standalone RAPT.