[2024-01-25 18:42:05,356] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:05,358] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:05,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb7077f1-be40-42ab-90d4-8b2be6e9cbca/dqc_reference
[2024-01-25 18:42:06,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:06,487] [INFO] Task started: Prodigal
[2024-01-25 18:42:06,487] [INFO] Running command: gunzip -c /var/lib/cwl/stg55faf5de-c307-4daa-8a19-2053b80cb19a/GCF_024006985.1_ASM2400698v1_genomic.fna.gz | prodigal -d GCF_024006985.1_ASM2400698v1_genomic.fna/cds.fna -a GCF_024006985.1_ASM2400698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:21,829] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:21,829] [INFO] Task started: HMMsearch
[2024-01-25 18:42:21,829] [INFO] Running command: hmmsearch --tblout GCF_024006985.1_ASM2400698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb7077f1-be40-42ab-90d4-8b2be6e9cbca/dqc_reference/reference_markers.hmm GCF_024006985.1_ASM2400698v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:22,029] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:22,030] [INFO] Found 6/6 markers.
[2024-01-25 18:42:22,056] [INFO] Query marker FASTA was written to GCF_024006985.1_ASM2400698v1_genomic.fna/markers.fasta
[2024-01-25 18:42:22,056] [INFO] Task started: Blastn
[2024-01-25 18:42:22,056] [INFO] Running command: blastn -query GCF_024006985.1_ASM2400698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb7077f1-be40-42ab-90d4-8b2be6e9cbca/dqc_reference/reference_markers.fasta -out GCF_024006985.1_ASM2400698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:22,612] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:22,615] [INFO] Selected 26 target genomes.
[2024-01-25 18:42:22,615] [INFO] Target genome list was writen to GCF_024006985.1_ASM2400698v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:22,630] [INFO] Task started: fastANI
[2024-01-25 18:42:22,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg55faf5de-c307-4daa-8a19-2053b80cb19a/GCF_024006985.1_ASM2400698v1_genomic.fna.gz --refList GCF_024006985.1_ASM2400698v1_genomic.fna/target_genomes.txt --output GCF_024006985.1_ASM2400698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:37,822] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:37,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb7077f1-be40-42ab-90d4-8b2be6e9cbca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:37,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb7077f1-be40-42ab-90d4-8b2be6e9cbca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:37,832] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:42:37,832] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:42:37,832] [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	77.5491	316	1066	95	below_threshold
Robiginitalea biformata	strain=HTCC2501	GCA_000024125.1	252307	252307	type	True	77.3781	289	1066	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.6762	59	1066	95	below_threshold
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	76.5893	115	1066	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	76.5562	59	1066	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.4719	87	1066	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.4385	74	1066	95	below_threshold
Robiginitalea myxolifaciens	strain=DSM 21019	GCA_900115205.1	400055	400055	type	True	76.3749	120	1066	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	76.1791	73	1066	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	76.1742	73	1066	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.1708	68	1066	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	76.1567	60	1066	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	76.1567	60	1066	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	76.1254	73	1066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:37,833] [INFO] DFAST Taxonomy check result was written to GCF_024006985.1_ASM2400698v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:37,834] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:37,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:37,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb7077f1-be40-42ab-90d4-8b2be6e9cbca/dqc_reference/checkm_data
[2024-01-25 18:42:37,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:37,868] [INFO] Task started: CheckM
[2024-01-25 18:42:37,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024006985.1_ASM2400698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024006985.1_ASM2400698v1_genomic.fna/checkm_input GCF_024006985.1_ASM2400698v1_genomic.fna/checkm_result
[2024-01-25 18:43:20,786] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:20,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:20,832] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:20,832] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:20,832] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024006985.1_ASM2400698v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:20,833] [INFO] Task started: Blastn
[2024-01-25 18:43:20,833] [INFO] Running command: blastn -query GCF_024006985.1_ASM2400698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb7077f1-be40-42ab-90d4-8b2be6e9cbca/dqc_reference/reference_markers_gtdb.fasta -out GCF_024006985.1_ASM2400698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:21,657] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:21,660] [INFO] Selected 20 target genomes.
[2024-01-25 18:43:21,661] [INFO] Target genome list was writen to GCF_024006985.1_ASM2400698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:21,685] [INFO] Task started: fastANI
[2024-01-25 18:43:21,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg55faf5de-c307-4daa-8a19-2053b80cb19a/GCF_024006985.1_ASM2400698v1_genomic.fna.gz --refList GCF_024006985.1_ASM2400698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024006985.1_ASM2400698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:34,154] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:34,162] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:43:34,162] [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_014243345.1	s__Robiginitalea sp014243345	77.5953	300	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198115.1	s__Robiginitalea sediminis	77.5491	316	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024125.1	s__Robiginitalea biformata	77.3781	289	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227965.1	s__Robiginitalea sp006227965	77.3456	187	1066	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	76.6899	164	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638095.1	s__Muriicola marianensis	76.5893	115	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	76.4719	87	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003058265.1	s__Muricauda sp003058265	76.4385	74	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115205.1	s__Robiginitalea myxolifaciens	76.3749	120	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584105.1	s__Muricauda taeanensis	76.1742	73	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCA_009901585.1	s__R33 sp009901585	76.1708	68	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	76.0823	69	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:34,172] [INFO] GTDB search result was written to GCF_024006985.1_ASM2400698v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:34,172] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:34,175] [INFO] DFAST_QC result json was written to GCF_024006985.1_ASM2400698v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:34,176] [INFO] DFAST_QC completed!
[2024-01-25 18:43:34,176] [INFO] Total running time: 0h1m29s