[2024-01-24 13:25:31,144] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,147] [INFO] DQC Reference Directory: /var/lib/cwl/stgde325c5a-6a6e-4c78-a87b-0648c5194276/dqc_reference
[2024-01-24 13:25:32,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,469] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg196e2fa5-880e-4f46-b57f-22a8e542d84a/GCF_002198115.1_ASM219811v1_genomic.fna.gz | prodigal -d GCF_002198115.1_ASM219811v1_genomic.fna/cds.fna -a GCF_002198115.1_ASM219811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:50,742] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:50,742] [INFO] Task started: HMMsearch
[2024-01-24 13:25:50,743] [INFO] Running command: hmmsearch --tblout GCF_002198115.1_ASM219811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde325c5a-6a6e-4c78-a87b-0648c5194276/dqc_reference/reference_markers.hmm GCF_002198115.1_ASM219811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:51,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:51,045] [INFO] Found 6/6 markers.
[2024-01-24 13:25:51,076] [INFO] Query marker FASTA was written to GCF_002198115.1_ASM219811v1_genomic.fna/markers.fasta
[2024-01-24 13:25:51,076] [INFO] Task started: Blastn
[2024-01-24 13:25:51,077] [INFO] Running command: blastn -query GCF_002198115.1_ASM219811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde325c5a-6a6e-4c78-a87b-0648c5194276/dqc_reference/reference_markers.fasta -out GCF_002198115.1_ASM219811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:51,708] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:51,711] [INFO] Selected 16 target genomes.
[2024-01-24 13:25:51,712] [INFO] Target genome list was writen to GCF_002198115.1_ASM219811v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:51,722] [INFO] Task started: fastANI
[2024-01-24 13:25:51,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg196e2fa5-880e-4f46-b57f-22a8e542d84a/GCF_002198115.1_ASM219811v1_genomic.fna.gz --refList GCF_002198115.1_ASM219811v1_genomic.fna/target_genomes.txt --output GCF_002198115.1_ASM219811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:03,159] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:03,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde325c5a-6a6e-4c78-a87b-0648c5194276/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:03,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde325c5a-6a6e-4c78-a87b-0648c5194276/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:03,178] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:03,178] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:03,179] [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
Robiginitalea sediminis	strain=O458	GCA_002198115.1	1982593	1982593	type	True	100.0	1094	1095	95	conclusive
Robiginitalea biformata	strain=HTCC2501	GCA_000024125.1	252307	252307	type	True	77.926	372	1095	95	below_threshold
Robiginitalea myxolifaciens	strain=DSM 21019	GCA_900115205.1	400055	400055	type	True	76.9418	198	1095	95	below_threshold
Sinomicrobium kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	76.5706	51	1095	95	below_threshold
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	76.5473	133	1095	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.5302	89	1095	95	below_threshold
Muriicola jejuensis	strain=KCTC 22299	GCA_010671595.1	504488	504488	type	True	76.5165	141	1095	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.4416	99	1095	95	below_threshold
Zeaxanthinibacter enoshimensis	strain=DSM 18435	GCA_004362865.1	392009	392009	type	True	76.3177	109	1095	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	76.2649	64	1095	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_018863395.1	2842200	2842200	type	True	76.2439	67	1095	95	below_threshold
Sinomicrobium pectinilyticum	strain=5DNS001	GCA_003725735.1	1084421	1084421	type	True	76.0607	50	1095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:03,180] [INFO] DFAST Taxonomy check result was written to GCF_002198115.1_ASM219811v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:03,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:03,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:03,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde325c5a-6a6e-4c78-a87b-0648c5194276/dqc_reference/checkm_data
[2024-01-24 13:26:03,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:03,221] [INFO] Task started: CheckM
[2024-01-24 13:26:03,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002198115.1_ASM219811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002198115.1_ASM219811v1_genomic.fna/checkm_input GCF_002198115.1_ASM219811v1_genomic.fna/checkm_result
[2024-01-24 13:26:53,415] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:53,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:53,440] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:53,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:53,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002198115.1_ASM219811v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:53,441] [INFO] Task started: Blastn
[2024-01-24 13:26:53,442] [INFO] Running command: blastn -query GCF_002198115.1_ASM219811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde325c5a-6a6e-4c78-a87b-0648c5194276/dqc_reference/reference_markers_gtdb.fasta -out GCF_002198115.1_ASM219811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:54,195] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:54,199] [INFO] Selected 13 target genomes.
[2024-01-24 13:26:54,199] [INFO] Target genome list was writen to GCF_002198115.1_ASM219811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:54,266] [INFO] Task started: fastANI
[2024-01-24 13:26:54,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg196e2fa5-880e-4f46-b57f-22a8e542d84a/GCF_002198115.1_ASM219811v1_genomic.fna.gz --refList GCF_002198115.1_ASM219811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002198115.1_ASM219811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:02,283] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:02,297] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:02,297] [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_002198115.1	s__Robiginitalea sediminis	100.0	1094	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000024125.1	s__Robiginitalea biformata	77.9347	371	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243345.1	s__Robiginitalea sp014243345	77.869	399	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115205.1	s__Robiginitalea myxolifaciens	76.9418	198	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683825.1	s__Zeaxanthinibacter sp001683825	76.6433	187	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	76.5302	89	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_014638095.1	s__Muriicola marianensis	76.5298	134	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671595.1	s__Muriicola jejuensis	76.5165	141	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362865.1	s__Zeaxanthinibacter enoshimensis	76.3177	109	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:02,299] [INFO] GTDB search result was written to GCF_002198115.1_ASM219811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:02,300] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:02,305] [INFO] DFAST_QC result json was written to GCF_002198115.1_ASM219811v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:02,305] [INFO] DFAST_QC completed!
[2024-01-24 13:27:02,306] [INFO] Total running time: 0h1m31s