script is Died at coverage_clustering.pl line 122, <STRAINS> line 913.

[Hedi65]

Dear user/developer

I am encountering the following error. Any help is appreciated.

[Wed Apr 2 09:19:45 2025] Strain clustering and assembly [6/8]

mkdir -p /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis

/home/User/OPERA-MS//tools_opera_ms/perl /home/User/OPERA-MS/bin/coverage_clustering.pl /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/megahit_assembly/final.contigs.fa /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/reference_clustering /home/User/OPERA-MS/OPERA-MS-DB /home/User/OPERA-MS/ /home/User/OPERA-MS//tools_opera_ms/ 1 2> /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/coverage_clustering.err

Error in during strain clustering. Please see /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/coverage_clustering.err for details.

**content of coverage_clustering.err file is

*** Open file OPERA-MS-DB/genomes_8/Aliarcobacter_sp017996075__GCA_017996075.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/OLB9_sp016714785__GCA_016714785.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_21/Hydrogenophaga_sp021729865__GCF_021729865.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Novosphingobium_sp020853995__GCA_020853995.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Propionicimonas_sp020846255__GCA_020846255.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/OLB14_sp016715195__GCA_016715195.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Novosphingobium_sp017987575__GCA_017987575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_21/Trichococcus_flocculiformis__GCF_900113645.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/UBA2383_sp022709365__GCA_022709365.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_19/Accumulibacter_phosphatis_G__GCF_012939955.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Novosphingobium_sp017987575__GCA_017987575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Desulfoprunum_sp020049575__GCA_020049575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_16/Methanomethylovorans_hollandica__GCF_000328665.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Novosphingobium_sp020853995__GCA_020853995.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_3/Acidovorax_defluvii__GCA_003268905.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Aliarcobacter_sp017996075__GCA_017996075.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/Giesbergeria_sp023954095__GCA_023954095.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rubrivivax_sp016707445__GCA_016707445.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_3/Acidovorax_defluvii__GCA_003268905.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_21/Trichococcus_flocculiformis__GCF_900113645.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Desulfobacillus_sp016791205__GCA_016791205.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/OLB14_sp016715195__GCA_016715195.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rhodoferax_C_sp016705575__GCA_016705575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Desulfobacillus_sp018262875__GCA_018262875.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Ornithinibacter_sp017989115__GCA_017989115.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/PHOS-HE28_sp016710685__GCA_016710685.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/ELB16-189_sp018063305__GCA_018063305.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rhodoferax_C_sp016705575__GCA_016705575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Novosphingobium_sp017987575__GCA_017987575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_3/Flavobacterium_sp003497625__GCA_003497625.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/ELB16-189_sp018063305__GCA_018063305.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKHK01_sp016708465__GCA_016708465.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/UBA2383_sp022709365__GCA_022709365.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Phosphoribacter_sp016715285__GCA_016715285.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Pedobacter_sp019752795__GCA_019752795.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_18/Giesbergeria_sp003096555__GCF_003096555.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rhodoferax_C_sp016705575__GCA_016705575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/UBA1038_sp023460055__GCA_023460055.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/JAGLSY01_sp023137005__GCA_023137005.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Phosphoribacter_sp016715285__GCA_016715285.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JJ008_sp016706055__GCA_016706055.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/ELB16-189_sp018063305__GCA_018063305.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_21/Propionivibrio_aalborgensis__GCF_900089945.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/UBA1038_sp023460055__GCA_023460055.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Novosphingobium_sp020853995__GCA_020853995.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_16/Pseudorhodobacter_B_sp000176015__GCF_000176015.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Arctic95D-9_sp018058245__GCA_018058245.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Arctic95D-9_sp018058245__GCA_018058245.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKHK01_sp016708465__GCA_016708465.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/PHOS-HE28_sp016710685__GCA_016710685.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_21/Nitrosomonas_sp022836435__GCF_022836435.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Pedobacter_sp019752795__GCA_019752795.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Rhodoferax_sp017997975__GCA_017997975.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_16/Methanomethylovorans_hollandica__GCF_000328665.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKAV01_sp016719135__GCA_016719135.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_17/Martelella_sp001578105__GCF_001578105.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rhodoferax_C_sp016705575__GCA_016705575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/PBB1_sp017986065__GCA_017986065.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Rhodoferax_sp017997975__GCA_017997975.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKHK01_sp016708465__GCA_016708465.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_7/Accumulibacter_sp017302455__GCA_017302455.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/ELB16-189_sp018063305__GCA_018063305.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/OLB14_sp016715195__GCA_016715195.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/PHOS-HE28_sp018057455__GCA_018057455.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_3/Draconibacterium_sp003516705__GCA_003516705.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Pedobacter_sp019752795__GCA_019752795.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Arctic95D-9_sp018058245__GCA_018058245.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_12/JG1575_sp024579835__GCA_024579835.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/OLB9_sp016714785__GCA_016714785.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rubrivivax_sp016707445__GCA_016707445.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_2/Sedimentibacter_sp002381185__GCA_002381185.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Novosphingobium_sp020853995__GCA_020853995.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_21/Trichococcus_flocculiformis__GCF_900113645.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rubrivivax_sp016707445__GCA_016707445.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_3/UBA10799_sp003452655__GCA_003452655.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rhodoferax_C_sp016705575__GCA_016705575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/Rubrivivax_sp022843905__GCA_022843905.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKHK01_sp016708465__GCA_016708465.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JJ008_sp016706055__GCA_016706055.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JJ008_sp016706055__GCA_016706055.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JJ008_sp016706055__GCA_016706055.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JJ008_sp016706055__GCA_016706055.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_4/Agitococcus_sp006546595__GCA_006546595.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Rhodoferax_sp017997975__GCA_017997975.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Phosphoribacter_hodrii__GCA_016707175.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rhodoferax_C_sp016705575__GCA_016705575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/UBA2383_sp022709365__GCA_022709365.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_19/Nocardioides_piscis__GCF_011300215.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKAV01_sp016719135__GCA_016719135.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/ELB16-189_sp018063305__GCA_018063305.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_2/HGW-BRC1-1_sp002842095__GCA_002842095.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKHK01_sp016708465__GCA_016708465.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_20/Micrococcus_cohnii__GCF_014205175.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/Niabella_sp023423285__GCA_023423285.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rubrivivax_sp016707445__GCA_016707445.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JJ008_sp016706055__GCA_016706055.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Desulfobacillus_sp018262875__GCA_018262875.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_21/Trichococcus_flocculiformis__GCF_900113645.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Propionicimonas_sp020846255__GCA_020846255.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_16/Thermomonas_fusca__GCF_000423885.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Arctic95D-9_sp018058245__GCA_018058245.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKAV01_sp016719135__GCA_016719135.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_21/Nitrosomonas_oligotropha_A__GCF_900106555.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/UBA1038_sp023460055__GCA_023460055.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_18/Nocardioides_glacieisoli__GCF_004137245.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/ELB16-189_sp018063305__GCA_018063305.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Novosphingobium_sp020848655__GCA_020848655.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/ELB16-189_sp018063305__GCA_018063305.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Austwickia_sp020161845__GCA_020161845.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Phosphoribacter_hodrii__GCA_016707175.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Phosphoribacter_sp016715285__GCA_016715285.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/OLB9_sp016714785__GCA_016714785.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Novosphingobium_sp017987575__GCA_017987575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKAV01_sp016719135__GCA_016719135.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/OLB9_sp016714785__GCA_016714785.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/PBB1_sp017986065__GCA_017986065.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKAV01_sp016719135__GCA_016719135.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_11/Giesbergeria_sp023954095__GCA_023954095.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_10/Sphingobium_sp022652485__GCA_022652485.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rubrivivax_sp016707445__GCA_016707445.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKHK01_sp016708465__GCA_016708465.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKAV01_sp016719135__GCA_016719135.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/ELB16-189_sp019638285__GCA_019638285.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/UBA7236_sp016718035__GCA_016718035.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Novosphingobium_sp020853995__GCA_020853995.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/PBB1_sp017986065__GCA_017986065.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Rhodoferax_sp017997975__GCA_017997975.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Desulfobacillus_sp018262875__GCA_018262875.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Desulfobacillus_sp018262875__GCA_018262875.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rhodoferax_C_sp016705575__GCA_016705575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rubrivivax_sp016707445__GCA_016707445.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Rhodoferax_sp017997975__GCA_017997975.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/OLB9_sp016714785__GCA_016714785.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_2/Desulfomicrobium_sp002412965__GCA_002412965.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Novosphingobium_sp017987575__GCA_017987575.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/UBA1573_sp018063145__GCA_018063145.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Rhodoferax_sp017997975__GCA_017997975.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_8/Arctic95D-9_sp018058245__GCA_018058245.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/JADKHK01_sp016708465__GCA_016708465.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/PHOS-HE28_sp016710685__GCA_016710685.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/OLB8_sp016711705__GCA_016711705.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Pedobacter_sp019752795__GCA_019752795.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Rubrivivax_sp016707445__GCA_016707445.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/UBA5066_sp016714815__GCA_016714815.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_6/Phosphoribacter_sp016715285__GCA_016715285.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_9/Pedobacter_sp019752795__GCA_019752795.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_19/Ornithinibacter_aureus__GCF_009858245.1_genomic.fna.gz
*** Open file OPERA-MS-DB/genomes_1/66-26_sp001897745__GCA_001897745.1_genomic.fna.gz
Died at /home/User/OPERA-MS/bin/coverage_clustering.pl line 122, line 913.

[jsgounot]

Hi Hedi,

could you please check if you fall into the same issue than here. Otherwise, it is potentially a memory error, could you check this as well?

Regards,
JS

[Hedi65]

Thanks for your reply. According to your recommendations, I created the DB correctly inside the main folder. Regarding memory, we have 500 GB of memory. Do you think it could still be causing the issue?

Best regards

[jsgounot]

Depending of the database and your sample. We noticed for users using very deep metagenomic sample in diverse environment such as soil, the memory usage can sometimes spike.

Edit: Could you check you can open and uncompress this file: OPERA-MS-DB/genomes_1/66-26_sp001897745__GCA_001897745.1_genomic.fna.gz?

[Hedi65]

Thanks for your tips

Interestingly, genome 1 was not present at all. I recreated the DB and re-ran the script. I can see that it created assembly and clustering for many different species, but at the end, I got another error

Error in during strain clustering assembly. Please see /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/*.log for details.

*Using the grep "Invalid version format" .log command, I found no invalid errors.

Below is the content for the latest created log file in the folder

*** End window construction
*** [1] 5346

[1] 19.11505 197.96553 457.72457
*** MODE DETECTED 5346 [1] 19.11505 197.96553 457.72457

MODE_INFO 457.72457 31.9358892 472.520477983792 [312 666]
MODE_EVAL 457.72457 31.9358892 472.520477983792 11900 343.714285714286 0.727406116198154 1,375.63

MODE_INFO 197.96553 31.9358892 204.364749001599 [132 291]
MODE_EVAL 197.96553 31.9358892 204.364749001599 821440 198.972268211921 0.973613449403467 1,743.95
MODE_IMPROVEMENT 197.96553 206.004758409419 25.6249415886801 [127 303]

MODE_INFO 19.11505 31.9358892 19.7329423733668 [9 32]
MODE_EVAL 19.11505 31.9358892 19.7329423733668 345440 18.8956692913386 0.957569780208842 100.83
MODE_IMPROVEMENT 19.11505 24.8080748651363 4.35762629758732 [5 57]

MODE_INFO 5346 31.9358892 5518.80899751865 [3698 7711]
*** End mode detection
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i0/pairedEdges_i0

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i0
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i1/pairedEdges_i1

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i1
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i2/pairedEdges_i2

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i2
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i3/pairedEdges_i3

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i3
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i4/pairedEdges_i4

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i4
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i5/pairedEdges_i5

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i5
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i0/pairedEdges_i0

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i0
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i1/pairedEdges_i1

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i1
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i2/pairedEdges_i2

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i2
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i3/pairedEdges_i3

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i3
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i4/pairedEdges_i4

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i4
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/pairedEdges_i5/pairedEdges_i5

mkdir /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i5
*** OPERA-LG data generation

timeout 5m /home/User/OPERA-MS//OPERA-LG/bin/OPERA-LG /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/opera.config > /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/log.txt
*** Read ReadCoverageFile /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/contigs
min library mean : 250
minimum contig length is 500
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i0/pairedEdges_i0
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i1/pairedEdges_i1
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i2/pairedEdges_i2
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i3/pairedEdges_i3
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i4/pairedEdges_i4
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i5/pairedEdges_i5

/home/User/OPERA-MS//OPERA-LG/bin/OPERA-LG-fast /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/opera.config > /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/log_fast.txt
*** Read ReadCoverageFile /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/contigs
min library mean : 250
minimum contig length is 500
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i0/pairedEdges_i0
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i1/pairedEdges_i1
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i2/pairedEdges_i2
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i3/pairedEdges_i3
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i4/pairedEdges_i4
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_1/pairedEdges_i5/pairedEdges_i5

timeout 5m /home/User/OPERA-MS//OPERA-LG/bin/OPERA-LG /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/opera.config > /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/log.txt
*** Read ReadCoverageFile /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/contigs
min library mean : 250
minimum contig length is 500
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i0/pairedEdges_i0
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i1/pairedEdges_i1
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i2/pairedEdges_i2
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i3/pairedEdges_i3
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i4/pairedEdges_i4
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone01/intermediate_files/strain_analysis/Propionivibrio_dominans/STRAIN_2/pairedEdges_i5/pairedEdges_i5

[jsgounot]

Hi Hedi, I'll be on leave for a week and don't know exactly why you have this error right now. I hope this can wait for my return.

[jsgounot]

Hi Hedi,

if you don't mind, could you check the tail of not only the last file, but a few more? OPERA-MS runs multiple commands in parallel and it's possible that the last created log is not the related to your actual problem. Alternatively, you could run the intermediate_files/strain_analysis/assembly.cmd file with bash and check when it crash.

JS

[Hedi65]

Thank you for your comment, and I apologize for the delay in my reply. I was working remotely.

I added '/usr/bin/time -v' to my script to determine the maximum memory usage, and the maximum memory usage for the crash iterations is less than 50 GB. Considering that my system has 500 GB of memory, there is probably no memory issue.

Only 4 of my 7 samples crashed during the Strain clustering and assembly [6/8]. By running the assembly.cmd file, I can see that for one of the iterations *** *** Assembly Propionivibrio_aalborgensis 2, Elapsed time: 0 is the last output. I can't find the exact log file in the folder, but there are multiple Propionivibrio log files. Everything appears to be similar, without any specific errors. I am pasting some here

Propionivibrio_aalborgensis.log

*** End window construction
*** [1] 6273

[1] 41.27763 115.55914 236.67030 411.07038 427.21853 459.51484 495.04078
[8] 519.26302 593.54453 632.30010 711.42606 782.47794
*** MODE DETECTED 6273 [1] 41.27763 115.55914 236.67030 411.07038 427.21853 459.51484 495.04078 [8] 519.26302 593.54453 632.30010 711.42606 782.47794

MODE_INFO 782.47794 29.640207 809.798899656472 [529 1150]
MODE_EVAL 782.47794 29.640207 809.798899656472 1020 636 0.785380173114338 14,118

MODE_INFO 711.42606 29.640207 736.266175855308 [481 1046]
MODE_EVAL 711.42606 29.640207 736.266175855308 2720 471.125 0.639884073789893 57,635.36

MODE_INFO 632.30010 29.640207 654.377457890605 [427 930]
MODE_EVAL 632.30010 29.640207 654.377457890605 3060 466.333333333333 0.712636610124936 51,415.11

MODE_INFO 593.54453 29.640207 614.268700394439 [400 874]
MODE_EVAL 593.54453 29.640207 614.268700394439 4080 454 0.739090238048063 39,028.17

MODE_INFO 519.26302 29.640207 537.393580997691 [350 765]
MODE_EVAL 519.26302 29.640207 537.393580997691 8160 410.75 0.764337376783376 21,451.77

MODE_INFO 495.04078 29.640207 512.325598507073 [333 730]
MODE_EVAL 495.04078 29.640207 512.325598507073 11560 390.205882352941 0.761636512971456 17,546.58

MODE_INFO 459.51484 29.640207 475.559236606491 [309 678]
MODE_EVAL 459.51484 29.640207 475.559236606491 32640 344.40625 0.72421314420812 7,599.07

MODE_INFO 427.21853 29.640207 442.135270301493 [287 630]
MODE_EVAL 427.21853 29.640207 442.135270301493 121720 305.159217877095 0.690194242293781 1,749.83

MODE_INFO 411.07038 29.640207 425.423292323574 [276 607]
MODE_EVAL 411.07038 29.640207 425.423292323574 223720 294.209726443769 0.691569389247252 1,258.71

MODE_INFO 236.67030 29.640207 244.933868067088 [157 352]
MODE_EVAL 236.67030 29.640207 244.933868067088 1717000 241.776237623762 0.987108232649716 1,264.76
MODE_IMPROVEMENT 236.67030 240.885849966764 57.1422120164519 [173 319]

MODE_INFO 115.55914 29.640207 119.593997010635 [74 175]
MODE_EVAL 115.55914 29.640207 119.593997010635 47600 134.142857142857 1.12165209371611 2,195.22

MODE_INFO 41.27763 29.640207 42.7188776138877 [24 66]
MODE_EVAL 41.27763 29.640207 42.7188776138877 351560 45.1092843326886 1.05595668360968 166.76
MODE_IMPROVEMENT 41.27763 43.9023769412023 16.726327499249 [21 73]

MODE_INFO 6273 29.640207 6492.02774655225 [4279 9175]
*** End mode detection
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i0/pairedEdges_i0
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i1/pairedEdges_i1
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i2/pairedEdges_i2
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i3/pairedEdges_i3
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i4/pairedEdges_i4
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i5/pairedEdges_i5
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i0/pairedEdges_i0
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i1/pairedEdges_i1
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i2/pairedEdges_i2
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i3/pairedEdges_i3
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i4/pairedEdges_i4
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/pairedEdges_i5/pairedEdges_i5
*** OPERA-LG data generation

timeout 5m /home/User/OPERA-MS//OPERA-LG/bin/OPERA-LG /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_1/opera.config > /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_1/log.txt
*** Read ReadCoverageFile /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_1/contigs
min library mean : 250
minimum contig length is 500
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_1/pairedEdges_i0/pairedEdges_i0
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_1/pairedEdges_i1/pairedEdges_i1
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_1/pairedEdges_i2/pairedEdges_i2
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_1/pairedEdges_i3/pairedEdges_i3
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_1/pairedEdges_i4/pairedEdges_i4
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_1/pairedEdges_i5/pairedEdges_i5

timeout 5m /home/User/OPERA-MS//OPERA-LG/bin/OPERA-LG /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_2/opera.config > /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_2/log.txt
*** Read ReadCoverageFile /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_2/contigs
min library mean : 250
minimum contig length is 500
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_2/pairedEdges_i0/pairedEdges_i0
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_2/pairedEdges_i1/pairedEdges_i1
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_2/pairedEdges_i2/pairedEdges_i2
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_2/pairedEdges_i3/pairedEdges_i3
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_2/pairedEdges_i4/pairedEdges_i4
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_aalborgensis/STRAIN_2/pairedEdges_i5/pairedEdges_i5

Propionivibrio_sp907163075.log

*** End window construction
*** [1] 10205

[1] 10.20714 74.11235 146.00571 163.43440 185.22027 207.73233 225.16103
[8] 244.04211 260.74461 270.91135 297.78058 312.30449 334.81655
*** MODE DETECTED 10205 [1] 10.20714 74.11235 146.00571 163.43440 185.22027 207.73233 225.16103 [8] 244.04211 260.74461 270.91135 297.78058 312.30449 334.81655

MODE_INFO 334.81655 29.640207 346.506987502774 [224 495]

MODE_INFO 312.30449 29.640207 323.208897569401 [208 462]

MODE_INFO 297.78058 29.640207 308.17787147209 [198 441]

MODE_INFO 270.91135 29.640207 280.370476814272 [180 402]
MODE_EVAL 270.91135 29.640207 280.370476814272 2040 181.833333333333 0.648546649416966 1,290.47

MODE_INFO 260.74461 29.640207 269.848755441407 [173 387]
MODE_EVAL 260.74461 29.640207 269.848755441407 2040 181.833333333333 0.673834248506717 1,290.47

MODE_INFO 244.04211 29.640207 252.563071807294 [162 363]
MODE_EVAL 244.04211 29.640207 252.563071807294 2380 179.428571428571 0.710430745653409 1,140.82

MODE_INFO 225.16103 29.640207 233.022740985539 [149 335]
MODE_EVAL 225.16103 29.640207 233.022740985539 2380 179.428571428571 0.770004552644528 1,140.82

MODE_INFO 207.73233 29.640207 214.985501389439 [137 310]
MODE_EVAL 207.73233 29.640207 214.985501389439 3740 166.818181818182 0.775950846638707 1,040.33

MODE_INFO 185.22027 29.640207 191.687411456066 [122 277]
MODE_EVAL 185.22027 29.640207 191.687411456066 7140 146 0.761656693525036 1,429.24

MODE_INFO 163.43440 29.640207 169.14086713552 [107 245]
MODE_EVAL 163.43440 29.640207 169.14086713552 10200 135.4 0.800516175026546 1,346.97

MODE_INFO 146.00571 29.640207 151.10363788858 [95 219]
MODE_EVAL 146.00571 29.640207 151.10363788858 36040 110.518867924528 0.731411033306969 953.12

MODE_INFO 74.11235 29.640207 76.700053014856 [46 114]
MODE_EVAL 74.11235 29.640207 76.700053014856 3123240 75.8818854779012 0.989332894766104 213.46
MODE_IMPROVEMENT 74.11235 75.9264056297342 41.8545078691208 [48 108]

MODE_INFO 10.20714 29.640207 10.5635319771949 [4 19]
MODE_EVAL 10.20714 29.640207 10.5635319771949 189040 11.6546762589928 1.10329350866297 23.75
MODE_IMPROVEMENT 10.20714 11.2053367979963 11.2255787841523 [3 22]

MODE_INFO 10205 29.640207 10561.3172570645 [6964 14922]
*** End mode detection
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i0/pairedEdges_i0
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i1/pairedEdges_i1
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i2/pairedEdges_i2
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i3/pairedEdges_i3
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i4/pairedEdges_i4
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i5/pairedEdges_i5
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i0/pairedEdges_i0
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i1/pairedEdges_i1
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i2/pairedEdges_i2
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i3/pairedEdges_i3
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i4/pairedEdges_i4
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/pairedEdges_i5/pairedEdges_i5
*** OPERA-LG data generation

timeout 5m /home/User/OPERA-MS//OPERA-LG/bin/OPERA-LG /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_1/opera.config > /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_1/log.txt
*** Read ReadCoverageFile /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_1/contigs
min library mean : 250
minimum contig length is 500
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_1/pairedEdges_i0/pairedEdges_i0
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_1/pairedEdges_i1/pairedEdges_i1
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_1/pairedEdges_i2/pairedEdges_i2
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_1/pairedEdges_i3/pairedEdges_i3
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_1/pairedEdges_i4/pairedEdges_i4
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_1/pairedEdges_i5/pairedEdges_i5

timeout 5m /home/User/OPERA-MS//OPERA-LG/bin/OPERA-LG /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_2/opera.config > /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_2/log.txt
*** Read ReadCoverageFile /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_2/contigs
min library mean : 250
minimum contig length is 500
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_2/pairedEdges_i0/pairedEdges_i0
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_2/pairedEdges_i1/pairedEdges_i1
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_2/pairedEdges_i2/pairedEdges_i2
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_2/pairedEdges_i3/pairedEdges_i3
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_2/pairedEdges_i4/pairedEdges_i4
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp907163075/STRAIN_2/pairedEdges_i5/pairedEdges_i5

Propionivibrio_sp016790145.log

*** End window construction
*** [1] 2605

[1] 19.76583 99.42421 442.19663 520.64806
*** MODE DETECTED 2605 [1] 19.76583 99.42421 442.19663 520.64806

MODE_INFO 520.64806 29.640207 538.826980983357 [351 767]
MODE_EVAL 520.64806 29.640207 538.826980983357 1700 451.2 0.837374548647437 834.96

MODE_INFO 442.19663 29.640207 457.636344873569 [297 652]
MODE_EVAL 442.19663 29.640207 457.636344873569 7820 345 0.753873690026331 10,509.74

MODE_INFO 99.42421 29.640207 102.895700621559 [63 151]
MODE_EVAL 99.42421 29.640207 102.895700621559 405960 107.736180904523 1.04704259025133 1,368.04

MODE_INFO 19.76583 29.640207 20.4559727074183 [10 34]
MODE_EVAL 19.76583 29.640207 20.4559727074183 221000 20.2184615384615 0.988389153018834 117.24

MODE_INFO 2605 29.640207 2695.95604651181 [1774 3814]
*** End mode detection
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/pairedEdges_i0/pairedEdges_i0
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/pairedEdges_i1/pairedEdges_i1
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/pairedEdges_i2/pairedEdges_i2
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/pairedEdges_i3/pairedEdges_i3
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/pairedEdges_i4/pairedEdges_i4
*** Analyzing edge file /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/pairedEdges_i5/pairedEdges_i5
*** OPERA-LG data generation

timeout 5m /home/User/OPERA-MS//OPERA-LG/bin/OPERA-LG /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/STRAIN_1/opera.config > /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/STRAIN_1/log.txt
*** Read ReadCoverageFile /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/STRAIN_1/contigs
min library mean : 250
minimum contig length is 500
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/STRAIN_1/pairedEdges_i0/pairedEdges_i0
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/STRAIN_1/pairedEdges_i1/pairedEdges_i1
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/STRAIN_1/pairedEdges_i2/pairedEdges_i2
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/STRAIN_1/pairedEdges_i3/pairedEdges_i3
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/STRAIN_1/pairedEdges_i4/pairedEdges_i4
Analyzing file: /data2/User_HiAS/Hybrid/Hybrid_Zones_Opera/Zone04/intermediate_files/strain_analysis/Propionivibrio_sp016790145/STRAIN_1/pairedEdges_i5/pairedEdges_i5

[jsgounot]

Hi Hedi,

do you have a excluded_contigs.fa and contigs.fa in each of your strain directory?

JS

[Hedi65]

I have contigs.fa in my strain directory for all my samples, but excluded_contigs.fa is missing for some of the directories where the script crashed. I checked the samples where the script did not crash, and all the directories contained both excluded_contigs.fa and contigs.fa.

H

[jsgounot]

Hi Hedi,

I'm sorry but I don't know what could be the issue based on code alone. If you have time, for one of the species that did not work, please send me a tar.gz file of the species (intermediate_files/strain_analysis/{species_name}) and the command line to generate the folder as well that you can find in the intermediate_files/strain_analysis/assembly.cmd file. Thanks.

JS

[Hedi65]

Agitococcus.tar.gz
assembly.tar.gz

i appreciate your support. requested folder and file attached.

[jsgounot]

Hi Hedi,

It seems you have the same issue than #96 . Some of the species (like Agitococcus_sp002333125) does not have a reference genome size, which is likely due to some database generation error. Please check your database like I suggested in the other issue. Let me know if you still have a problem.

Regards,
JS