diff test-data/test2.log @ 16:a3b35edea53a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
author iuc
date Tue, 12 Nov 2024 12:46:19 +0000
parents 3061c8b029e5
children
line wrap: on
line diff
--- a/test-data/test2.log	Thu Mar 02 10:38:54 2023 +0000
+++ b/test-data/test2.log	Tue Nov 12 12:46:19 2024 +0000
@@ -1,34 +1,34 @@
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat --features /tmp/tmphjbhe4x0/files/3/1/a/dataset_31a7a886-1c84-4423-8fc9-cdfda1537f40.dat --operons /tmp/tmphjbhe4x0/files/2/9/8/dataset_29831cd9-b20d-4b69-af42-19aa1c84bbbb.dat --circos --k-mer-stats --k-mer-size 101 --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat --threads 1
+/usr/local/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat --features /tmp/tmplvd_uy2v/files/a/3/1/dataset_a314adcb-6b74-48ce-9b09-e2eba7a43bd1.dat --operons /tmp/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.dat --circos --k-mer-stats --k-mer-size 101 --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.dat --threads 1
 
-Version: 5.2.0
+Version: 5.3.0
 
 System information:
-  OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64)
-  Python version: 3.9.13
-  CPUs number: 8
+  OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64)
+  Python version: 3.12.3
+  CPUs number: 12
 
-Started: 2022-07-07 16:53:46
+Started: 2024-11-12 11:21:53
 
-Logging to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log
+Logging to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log
 WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
 
-CWD: /tmp/tmphjbhe4x0/job_working_directory/000/12/working
+CWD: /tmp/tmplvd_uy2v/job_working_directory/000/12/working
 Main parameters: 
   MODE: default, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \
   ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000
 
 Reference:
-  /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat ==> dataset_adad470c-d758-46ef-afd5-390f178fb362
+  /tmp/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat ==> dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39
 
 Contigs:
   Pre-processing...
-  1  /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat ==> contig1
-  2  /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat ==> contig2
+  1  /tmp/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat ==> contig1
+  2  /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.dat ==> contig2
 
-2022-07-07 16:53:55
+2024-11-12 11:21:54
 Running Basic statistics processor...
   Reference genome:
-    dataset_adad470c-d758-46ef-afd5-390f178fb362.dat, length = 6650, num fragments = 1, GC % = 52.00
+    dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat, length = 6650, num fragments = 1, GC % = 52.00
   Contig files: 
     1  contig1
     2  contig2
@@ -36,164 +36,164 @@
     1  contig1, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp =  0.00
     2  contig2, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp =  0.00
   Drawing Nx plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf
   Drawing NGx plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf
   Drawing cumulative plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf
   Drawing GC content plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf
   Drawing contig1 GC content plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf
   Drawing contig2 GC content plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf
 Done.
 
-2022-07-07 16:53:58
+2024-11-12 11:21:54
 Running analysis based on unique 101-mers...
+NOTICE: Permission denied accessing /usr/local/lib/python3.12/site-packages/quast_libs/kmc. KMC will be downloaded to home directory /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast
+Downloading KMC (file: kmc)...
+KMC successfully downloaded!
+Downloading KMC (file: kmc_tools)...
+KMC successfully downloaded!
   Running KMC on reference...
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \
--t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \
-outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc outputdir/k_mer_stats/tmp \
+/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
+-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \
+outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp \
 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
--t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \
-outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc.histo.txt \
+/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
+outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc.histo.txt \
 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
   Analyzing assemblies completeness...
     1  contig1
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \
--t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \
+/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
+-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \
 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
--t1 -hp simple outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \
-outputdir/k_mer_stats/tmp/contig1.kmc intersect outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \
+/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \
+outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig1.kmc \
+intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc >> \
+outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
+/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
+outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc.histo.txt \
 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
--t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \
-outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc.histo.txt >> \
-outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
     2  contig2
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \
--t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \
+/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
+-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \
 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
--t1 -hp simple outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \
-outputdir/k_mer_stats/tmp/contig2.kmc intersect outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc \
+/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \
+outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig2.kmc \
+intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc >> \
+outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
+/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
+outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc.histo.txt \
 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
--t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc \
-outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc.histo.txt >> \
-outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
   Analyzing assemblies correctness...
     Downsampling k-mers...
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
--t1 -hp filter outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \
-outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.fasta -ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.filtered.fasta \
->> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
+/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp filter \
+outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.fasta \
+-ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.filtered.fasta >> outputdir/k_mer_stats/kmc.log \
+2>> outputdir/k_mer_stats/kmc.err
     1  contig1
-  /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \
-  -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \
-  > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err
+  /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 \
+  outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \
+  2>> outputdir/k_mer_stats/kmc.err
     2  contig2
-  /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \
-  -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \
-  > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err
+  /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 \
+  outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \
+  2>> outputdir/k_mer_stats/kmc.err
   Creating total report...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex
 Done.
 
-2022-07-07 16:54:01
+2024-11-12 11:21:55
 Running Contig analyzer...
   1  contig1
-  1  Logging to files /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr...
+  1  Logging to files /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr...
   1  Aligning contigs to the reference
-  1  /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \
-     -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \
-     0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \
+  1  /usr/local/bin/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s \
+     65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \
      outputdir/quast_corrected_input/contig1 > outputdir/contigs_reports/minimap_output/contig1.coords_tmp \
      2>> outputdir/contigs_reports/contigs_report_contig1.stderr
   1  Analysis is finished.
 
   2  contig2
-  2  Logging to files /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr...
+  2  Logging to files /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr...
   2  Aligning contigs to the reference
-  2  /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \
-     -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \
-     0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \
+  2  /usr/local/bin/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s \
+     65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \
      outputdir/quast_corrected_input/contig2 > outputdir/contigs_reports/minimap_output/contig2.coords_tmp \
      2>> outputdir/contigs_reports/contigs_report_contig2.stderr
   2  Analysis is finished.
 
   Creating total report...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
   Transposed version of total report...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
   Creating total report...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
   Drawing misassemblies by types plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf
   Drawing misassemblies FRCurve plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf
 Done.
 
-2022-07-07 16:54:01
+2024-11-12 11:21:55
 Running NA-NGA calculation...
   1  contig1, Largest alignment = 2030, NA50 = 1610, NGA50 = 1610, LA50 = 2, LGA50 = 2
   2  contig2, Largest alignment = 6650, NA50 = 6650, NGA50 = 6650, LA50 = 1, LGA50 = 1
   Drawing cumulative plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf
   Drawing NAx plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf
   Drawing NGAx plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf
 Done.
 
-2022-07-07 16:54:02
+2024-11-12 11:21:56
 Running Genome analyzer...
   Loaded 14 genomic features of type "ANY"
   NOTICE: Reference name in file with genomic features of type "ANY" (NC_000913.3) does not match the name in the reference file (NC_000913.3_1-6650). QUAST will ignore this issue and count as if they match.
 WARNING: Incorrect format of operon's file! GFF, NCBI and the plain TXT format accepted. See manual.
-WARNING: /tmp/tmphjbhe4x0/files/2/9/8/dataset_29831cd9-b20d-4b69-af42-19aa1c84bbbb.dat was skipped
+WARNING: /tmp/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.dat was skipped
   WARNING: No genomic features of type "operon" were loaded.
   1  contig1
   1  Analysis is finished.
   2  contig2
   2  Analysis is finished.
   Drawing genomic features cumulative plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf
   Drawing genomic features FRCurve plot...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf
   Drawing # complete genomic features histogram...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf
   Drawing Genome fraction, % histogram...
-    saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf
+    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf
 Done.
 
 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
 
-2022-07-07 16:54:04
+2024-11-12 11:21:56
 Creating large visual summaries...
 This may take a while: press Ctrl-C to skip this step..
   1 of 3: Creating PDF with all tables and plots...
   2 of 3: Creating Icarus viewers...
   3 of 3: Creating Circos plot...
-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/circos \
--conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err
+/usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \
+2> outputdir/circos/circos.err
 Done
 
-2022-07-07 16:54:16
+2024-11-12 11:22:00
 RESULTS:
-  Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex
-  Text versions of transposed total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
-  HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.html
-  PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.pdf
-  Circos plot is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)
-  Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/icarus.html
-  Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log
+  Text versions of total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex
+  Text versions of transposed total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
+  HTML version (interactive tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.html
+  PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.pdf
+  Circos plot is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)
+  Icarus (contig browser) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/icarus.html
+  Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log
 
-Finished: 2022-07-07 16:54:16
-Elapsed time: 0:00:30.044753
-NOTICEs: 2; WARNINGs: 4; non-fatal ERRORs: 0
+Finished: 2024-11-12 11:22:00
+Elapsed time: 0:00:07.048981
+NOTICEs: 3; WARNINGs: 4; non-fatal ERRORs: 0
 
 Thank you for using QUAST!