Error with ggr

[ingridvanw]

Dear developers,

I'm trying to use your tools for core SNP analysis. There are around 170 genomes, all of the same species.
The tutorial works fine but when I run my samples I have this error message.
It seems that there is a problem with ggr? The reference strain and genomes are recognized. It looks like that parsnp has finished core genome alignment (.maf, .xmfa, parsnpAligner.ini are generated), but the parsnp.ggrfile is empty (file is created but there stands "Cap'n Protox"). I tried to run with and withouth -c parameter, but the same error appears. Not sure what the problem is and how to solve this.
Can you please help me?

Parsnp version 2.1.3 is used. ParSNP is installed with conda.

parsnp -d *.fna -n mafft -c -r /ReferenceStrain/GCF_000014985.1_ASM1498v1_genomic.fna -p 8 -o /ParSNP/ --fo

---

SETTINGS:
|-refgenome: /data/GCF_000014985.1/GCF_000014985.1_ASM1498v1_genomic.fna
|-genomes:
/FastaFiles/run10_MT21-0984_S12.fna
/FastaFiles/run10_MV21-1157_S3.fna
...94 more file(s)...
/FastaFiles/run9_MV20-3580_S8.fna
/FastaFiles/run9_MV20-5582_S12.fna
|-aligner: mafft
|-outdir: /ParSNP/
|-OS: Linux
|-threads: 8

---

0:17:29 - INFO - <>
10:17:29 - INFO - No genbank file provided for reference annotations, skipping..
10:17:32 - INFO - Setting the partition size to 53
10:17:32 - INFO - Running partitions...
10:17:32 - INFO - 0%| | 0/3 [00:00<?, ?it/s]
10:21:53 - INFO - 33%|###3 | 1/3 [04:21<08:43, 261.91s/it]
10:21:58 - INFO - 67%|######6 | 2/3 [04:26<02:13, 133.15s/it]
10:21:58 - INFO - Computing intersection of all partition LCBs...
10:22:03 - INFO - Partition stats: Mean bp covered = 4057039.67 Mean LCB count = 2363.67
10:22:03 - INFO - After intersection: 3759727 reference bases over 3544 clusters
10:22:03 - INFO - Trimming partitioned XMFAs back to intersected intervals...
10:22:03 - INFO - 0%| | 0/3 [00:00<?, ?it/s]
10:27:11 - INFO - 33%|###3 | 1/3 [05:08<10:16, 308.07s/it]
10:27:23 - INFO - 100%|##########| 3/3 [05:19<00:00, 84.03s/it]
10:27:23 - INFO - 100%|##########| 3/3 [05:19<00:00, 106.44s/it]
10:27:23 - INFO - Merging trimmed XMFA files...
10:27:23 - INFO - 0%| | 0/3544 [00:00<?, ?it/s]
10:27:28 - INFO - 2%|1 | 54/3544 [00:05<05:23, 10.78it/s]
10:27:33 - INFO - 3%|3 | 118/3544 [00:10<04:46, 11.96it/s]
10:27:38 - INFO - 5%|5 | 182/3544 [00:15<04:32, 12.32it/s]
10:27:45 - INFO - 7%|6 | 244/3544 [00:21<05:05, 10.79it/s]
10:27:50 - INFO - 9%|8 | 304/3544 [00:26<04:49, 11.18it/s]
10:27:55 - INFO - 10%|# | 363/3544 [00:31<04:39, 11.37it/s]
10:28:00 - INFO - 12%|#1 | 421/3544 [00:37<04:44, 10.97it/s]
10:28:05 - INFO - 14%|#3 | 485/3544 [00:42<04:26, 11.46it/s]
10:28:10 - INFO - 15%|#5 | 548/3544 [00:47<04:14, 11.75it/s]
10:28:17 - INFO - 17%|#7 | 608/3544 [00:54<04:32, 10.78it/s]
10:28:23 - INFO - 19%|#8 | 663/3544 [01:00<04:35, 10.44it/s]
10:28:28 - INFO - 20%|## | 722/3544 [01:05<04:21, 10.81it/s]
10:28:33 - INFO - 22%|##2 | 785/3544 [01:10<04:04, 11.31it/s]
10:28:39 - INFO - 24%|##3 | 843/3544 [01:16<04:12, 10.69it/s]
10:28:44 - INFO - 25%|##5 | 902/3544 [01:21<04:01, 10.92it/s]
10:28:50 - INFO - 27%|##7 | 958/3544 [01:27<04:14, 10.14it/s]
10:28:55 - INFO - 29%|##8 | 1014/3544 [01:32<04:02, 10.43it/s]
10:29:01 - INFO - 30%|### | 1067/3544 [01:38<04:00, 10.32it/s]
10:29:07 - INFO - 32%|###1 | 1120/3544 [01:44<04:10, 9.68it/s]
10:29:13 - INFO - 33%|###3 | 1170/3544 [01:50<04:13, 9.36it/s]
10:29:18 - INFO - 35%|###5 | 1242/3544 [01:55<03:34, 10.71it/s]
10:29:23 - INFO - 37%|###6 | 1304/3544 [02:00<03:20, 11.17it/s]
10:29:29 - INFO - 38%|###8 | 1361/3544 [02:05<03:20, 10.87it/s]
10:29:34 - INFO - 40%|#### | 1419/3544 [02:11<03:13, 10.99it/s]
10:29:39 - INFO - 42%|####2 | 1489/3544 [02:16<02:53, 11.82it/s]
10:29:45 - INFO - 44%|####3 | 1549/3544 [02:22<02:57, 11.25it/s]
10:29:50 - INFO - 45%|####5 | 1606/3544 [02:27<02:52, 11.24it/s]
10:29:55 - INFO - 47%|####6 | 1663/3544 [02:32<02:50, 11.02it/s]
10:30:00 - INFO - 49%|####8 | 1719/3544 [02:37<02:46, 10.99it/s]
10:30:05 - INFO - 50%|##### | 1776/3544 [02:42<02:39, 11.10it/s]
10:30:12 - INFO - 52%|#####1 | 1832/3544 [02:48<02:45, 10.33it/s]
10:30:17 - INFO - 53%|#####3 | 1885/3544 [02:54<02:41, 10.27it/s]
10:30:22 - INFO - 55%|#####4 | 1940/3544 [02:59<02:34, 10.35it/s]
10:30:29 - INFO - 56%|#####6 | 1993/3544 [03:05<02:41, 9.59it/s]
10:30:34 - INFO - 58%|#####7 | 2042/3544 [03:11<02:42, 9.22it/s]
10:30:40 - INFO - 59%|#####9 | 2092/3544 [03:16<02:34, 9.41it/s]
10:30:45 - INFO - 60%|###### | 2140/3544 [03:22<02:31, 9.28it/s]
10:30:50 - INFO - 62%|######1 | 2187/3544 [03:27<02:26, 9.28it/s]
10:30:55 - INFO - 64%|######3 | 2257/3544 [03:32<02:01, 10.62it/s]
10:31:00 - INFO - 66%|######5 | 2322/3544 [03:37<01:48, 11.27it/s]
10:31:05 - INFO - 67%|######7 | 2386/3544 [03:42<01:39, 11.67it/s]
10:31:12 - INFO - 69%|######8 | 2445/3544 [03:49<01:43, 10.62it/s]
10:31:18 - INFO - 71%|####### | 2500/3544 [03:55<01:42, 10.15it/s]
10:31:23 - INFO - 72%|#######2 | 2552/3544 [04:00<01:38, 10.07it/s]
10:31:28 - INFO - 74%|#######3 | 2611/3544 [04:05<01:28, 10.54it/s]
10:31:33 - INFO - 76%|#######5 | 2681/3544 [04:10<01:15, 11.38it/s]
10:31:38 - INFO - 77%|#######7 | 2742/3544 [04:15<01:09, 11.60it/s]
10:31:43 - INFO - 79%|#######9 | 2811/3544 [04:20<01:00, 12.18it/s]
10:31:48 - INFO - 81%|########1 | 2878/3544 [04:25<00:53, 12.51it/s]
10:31:53 - INFO - 83%|########3 | 2949/3544 [04:30<00:45, 12.99it/s]
10:31:59 - INFO - 85%|########5 | 3023/3544 [04:36<00:39, 13.30it/s]
10:32:05 - INFO - 87%|########7 | 3090/3544 [04:42<00:35, 12.67it/s]
10:32:10 - INFO - 89%|########8 | 3154/3544 [04:47<00:30, 12.66it/s]
10:32:17 - INFO - 91%|######### | 3218/3544 [04:54<00:29, 11.13it/s]
10:32:23 - INFO - 92%|#########2| 3276/3544 [05:00<00:25, 10.65it/s]
10:32:29 - INFO - 94%|#########3| 3331/3544 [05:06<00:20, 10.52it/s]
10:32:34 - INFO - 96%|#########5| 3386/3544 [05:11<00:14, 10.62it/s]
10:32:39 - INFO - 98%|#########7| 3457/3544 [05:16<00:07, 11.57it/s]
10:32:44 - INFO - 99%|#########9| 3516/3544 [05:21<00:02, 11.19it/s]
10:32:48 - INFO - 100%|##########| 3544/3544 [05:24<00:00, 10.90it/s]
10:33:50 - CRITICAL - The following command failed:
>>$ harvesttools -q -o parsnp.ggr -f GCF_000014985.1_ASM1498v1_genomic.fna.ref -x parsnp.xmfa
Please veryify input data and restart Parsnp.
If the problem persists please contact the Parsnp development team.

  STDOUT:
  

  STDERR:
  zpipe: 

which harvesttools
/home/miniconda3/envs/parsnp/bin/harvesttools

harvesttools -h
gives back all harvesttools options

conda config --show channels

• conda-forge
• bioconda
• defaults

folders created:

• config
• log
• temp
• parsnp.ggr [only the value "Cap'n Protox" in there]
• parsnp.maf
• parnsp.xmfa
• parsnpAligner.ini

Kind regards,
ingrid

[ingridvanw]

@bkille , not sure who to tag, but I was hoping you can help me
Thanks in advance!

Kind regards,
Ingrid

[bkille]

Hi @ingridvanw

The command that fails is

harvesttools -q -o parsnp.ggr -f GCF_000014985.1_ASM1498v1_genomic.fna.ref -x parsnp.xmfa

I'm not sure how parsnp even ends up running that command, as there is no output directory present. The command is generated via the f-string

 f"harvesttools -q -o {outputDir}/parsnp.ggr -f {ref} -x {parsnp_output}"

I plan on releasing v2.1.4 this week, so please let me know if the issue persists after that. Also, you may try running parsnp in verbose mode, and or trying the command that fails by just copying it from the error message and pasting it to the command line. Please let me know if you have any other questions.

-Bryce