[2024-01-25 18:55:20,485] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:20,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:20,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e19b390-6ddd-48e5-8fac-1c5a8f43ad8b/dqc_reference
[2024-01-25 18:55:21,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:21,686] [INFO] Task started: Prodigal
[2024-01-25 18:55:21,686] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1ca55f2-e604-4627-b670-6b09be35b236/GCF_013761005.1_ASM1376100v1_genomic.fna.gz | prodigal -d GCF_013761005.1_ASM1376100v1_genomic.fna/cds.fna -a GCF_013761005.1_ASM1376100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:32,605] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:32,605] [INFO] Task started: HMMsearch
[2024-01-25 18:55:32,606] [INFO] Running command: hmmsearch --tblout GCF_013761005.1_ASM1376100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e19b390-6ddd-48e5-8fac-1c5a8f43ad8b/dqc_reference/reference_markers.hmm GCF_013761005.1_ASM1376100v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:32,859] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:32,860] [INFO] Found 6/6 markers.
[2024-01-25 18:55:32,890] [INFO] Query marker FASTA was written to GCF_013761005.1_ASM1376100v1_genomic.fna/markers.fasta
[2024-01-25 18:55:32,890] [INFO] Task started: Blastn
[2024-01-25 18:55:32,890] [INFO] Running command: blastn -query GCF_013761005.1_ASM1376100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e19b390-6ddd-48e5-8fac-1c5a8f43ad8b/dqc_reference/reference_markers.fasta -out GCF_013761005.1_ASM1376100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:33,435] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:33,443] [INFO] Selected 21 target genomes.
[2024-01-25 18:55:33,443] [INFO] Target genome list was writen to GCF_013761005.1_ASM1376100v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:33,468] [INFO] Task started: fastANI
[2024-01-25 18:55:33,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1ca55f2-e604-4627-b670-6b09be35b236/GCF_013761005.1_ASM1376100v1_genomic.fna.gz --refList GCF_013761005.1_ASM1376100v1_genomic.fna/target_genomes.txt --output GCF_013761005.1_ASM1376100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:49,804] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:49,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e19b390-6ddd-48e5-8fac-1c5a8f43ad8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:49,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e19b390-6ddd-48e5-8fac-1c5a8f43ad8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:49,810] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:49,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:49,810] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Desulfosalsimonas propionicica	strain=DSM 17721	GCA_013761005.1	332175	332175	type	True	100.0	1327	1329	95	conclusive
Desulfosudis oleivorans	strain=Hxd3	GCA_000018405.1	181663	181663	type	True	76.2899	101	1329	95	below_threshold
Desulfatitalea tepidiphila	strain=S28bF	GCA_001293685.1	1185843	1185843	type	True	76.1504	89	1329	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	76.1007	96	1329	95	below_threshold
Desulfosarcina alkanivorans	strain=PL12	GCA_009688945.1	571177	571177	type	True	75.7275	116	1329	95	below_threshold
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	75.7209	74	1329	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:49,811] [INFO] DFAST Taxonomy check result was written to GCF_013761005.1_ASM1376100v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:49,812] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:49,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:49,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e19b390-6ddd-48e5-8fac-1c5a8f43ad8b/dqc_reference/checkm_data
[2024-01-25 18:55:49,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:49,853] [INFO] Task started: CheckM
[2024-01-25 18:55:49,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013761005.1_ASM1376100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013761005.1_ASM1376100v1_genomic.fna/checkm_input GCF_013761005.1_ASM1376100v1_genomic.fna/checkm_result
[2024-01-25 18:56:23,671] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:23,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:23,694] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:23,694] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:23,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013761005.1_ASM1376100v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:23,695] [INFO] Task started: Blastn
[2024-01-25 18:56:23,695] [INFO] Running command: blastn -query GCF_013761005.1_ASM1376100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e19b390-6ddd-48e5-8fac-1c5a8f43ad8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013761005.1_ASM1376100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:24,555] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:24,558] [INFO] Selected 14 target genomes.
[2024-01-25 18:56:24,558] [INFO] Target genome list was writen to GCF_013761005.1_ASM1376100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:24,572] [INFO] Task started: fastANI
[2024-01-25 18:56:24,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1ca55f2-e604-4627-b670-6b09be35b236/GCF_013761005.1_ASM1376100v1_genomic.fna.gz --refList GCF_013761005.1_ASM1376100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013761005.1_ASM1376100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:33,192] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:33,205] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:33,205] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_013761005.1	s__Desulfosalsimonas propionicica	100.0	1327	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__Desulfosalsimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018224315.1	s__Desulfosalsimonas sp018224315	90.6086	570	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__Desulfosalsimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389605.1	s__Desulfosalsimonas sp011389605	79.6811	357	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__Desulfosalsimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018335195.1	s__Desulfosalsimonas sp018335195	79.0463	473	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__Desulfosalsimonas	95.0	99.35	99.35	0.95	0.95	2	-
GCA_018334855.1	s__Desulfosalsimonas sp018334855	78.0552	135	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__Desulfosalsimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390465.1	s__SURF-3 sp011390465	76.7262	158	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389935.1	s__B1SED10-16 sp011389935	76.5625	145	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__B1SED10-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900659855.1	s__CR-1 sp900659855	76.0458	71	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__CR-1;g__CR-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007136525.1	s__B1SED10-16 sp007136525	76.0298	50	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__B1SED10-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390065.1	s__JAABTD01 sp011390065	76.0033	114	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390985.1	s__JAABRJ01 sp011390985	75.9208	55	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAABRJ01;g__JAABRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218685.1	s__Desulfatitalea sp016218685	75.722	68	1329	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:33,206] [INFO] GTDB search result was written to GCF_013761005.1_ASM1376100v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:33,207] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:33,209] [INFO] DFAST_QC result json was written to GCF_013761005.1_ASM1376100v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:33,209] [INFO] DFAST_QC completed!
[2024-01-25 18:56:33,210] [INFO] Total running time: 0h1m13s