[2024-01-24 13:28:13,340] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:13,342] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:13,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg56776e35-615c-4324-805d-4c0cb125a3d6/dqc_reference
[2024-01-24 13:28:14,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,661] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg76282279-3679-4dee-9159-de929baa6974/GCF_022014595.1_ASM2201459v1_genomic.fna.gz | prodigal -d GCF_022014595.1_ASM2201459v1_genomic.fna/cds.fna -a GCF_022014595.1_ASM2201459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:33,326] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:33,327] [INFO] Task started: HMMsearch
[2024-01-24 13:28:33,327] [INFO] Running command: hmmsearch --tblout GCF_022014595.1_ASM2201459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56776e35-615c-4324-805d-4c0cb125a3d6/dqc_reference/reference_markers.hmm GCF_022014595.1_ASM2201459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:33,683] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:33,684] [INFO] Found 6/6 markers.
[2024-01-24 13:28:33,722] [INFO] Query marker FASTA was written to GCF_022014595.1_ASM2201459v1_genomic.fna/markers.fasta
[2024-01-24 13:28:33,722] [INFO] Task started: Blastn
[2024-01-24 13:28:33,722] [INFO] Running command: blastn -query GCF_022014595.1_ASM2201459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56776e35-615c-4324-805d-4c0cb125a3d6/dqc_reference/reference_markers.fasta -out GCF_022014595.1_ASM2201459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:34,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:34,362] [INFO] Selected 29 target genomes.
[2024-01-24 13:28:34,362] [INFO] Target genome list was writen to GCF_022014595.1_ASM2201459v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:34,377] [INFO] Task started: fastANI
[2024-01-24 13:28:34,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg76282279-3679-4dee-9159-de929baa6974/GCF_022014595.1_ASM2201459v1_genomic.fna.gz --refList GCF_022014595.1_ASM2201459v1_genomic.fna/target_genomes.txt --output GCF_022014595.1_ASM2201459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:54,195] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:54,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56776e35-615c-4324-805d-4c0cb125a3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:54,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56776e35-615c-4324-805d-4c0cb125a3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:54,214] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:54,214] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:54,214] [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
Solitalea longa	strain=HR-AV	GCA_002920915.1	2079460	2079460	type	True	79.4144	434	1467	95	below_threshold
Solitalea canadensis	strain=DSM 3403	GCA_000242635.3	995	995	type	True	78.8746	384	1467	95	below_threshold
Sphingobacterium spiritivorum	strain=FDAARGOS_1144	GCA_016725645.1	258	258	suspected-type	True	78.6808	50	1467	95	below_threshold
Solitalea koreensis	strain=DSM 21342	GCA_900182575.1	543615	543615	type	True	78.2452	214	1467	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_004025525.1	2233776	2233776	type	True	77.2348	50	1467	95	below_threshold
Mucilaginibacter auburnensis	strain=DSM 28175	GCA_002797815.1	1457233	1457233	type	True	77.2281	51	1467	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	77.1865	55	1467	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	77.0158	54	1467	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	76.6889	58	1467	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	76.632	60	1467	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	76.5281	52	1467	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	76.5281	52	1467	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	76.4012	52	1467	95	below_threshold
Mucilaginibacter aquatilis	strain=HME9299	GCA_009755275.1	1517760	1517760	type	True	76.3459	62	1467	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	76.2416	63	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:54,216] [INFO] DFAST Taxonomy check result was written to GCF_022014595.1_ASM2201459v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:54,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:54,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:54,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56776e35-615c-4324-805d-4c0cb125a3d6/dqc_reference/checkm_data
[2024-01-24 13:28:54,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:54,263] [INFO] Task started: CheckM
[2024-01-24 13:28:54,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022014595.1_ASM2201459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022014595.1_ASM2201459v1_genomic.fna/checkm_input GCF_022014595.1_ASM2201459v1_genomic.fna/checkm_result
[2024-01-24 13:29:50,394] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:50,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:50,416] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:50,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:50,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022014595.1_ASM2201459v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:50,417] [INFO] Task started: Blastn
[2024-01-24 13:29:50,417] [INFO] Running command: blastn -query GCF_022014595.1_ASM2201459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56776e35-615c-4324-805d-4c0cb125a3d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_022014595.1_ASM2201459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:51,238] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:51,242] [INFO] Selected 27 target genomes.
[2024-01-24 13:29:51,242] [INFO] Target genome list was writen to GCF_022014595.1_ASM2201459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:51,275] [INFO] Task started: fastANI
[2024-01-24 13:29:51,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg76282279-3679-4dee-9159-de929baa6974/GCF_022014595.1_ASM2201459v1_genomic.fna.gz --refList GCF_022014595.1_ASM2201459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022014595.1_ASM2201459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:12,739] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:12,757] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:30:12,757] [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_002920915.1	s__Solitalea longa	79.4355	435	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Solitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242635.2	s__Solitalea canadensis	78.8398	383	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Solitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190735.1	s__Pelobium saltans	78.2931	50	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182575.1	s__Solitalea koreensis	78.2452	214	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Solitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016724845.1	s__Sphingobacterium spiritivorum_A	77.9148	57	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.88	95.78	0.94	0.88	3	-
GCA_002151545.1	s__Pedobacter sp002151545	77.8155	55	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011303555.1	s__Pedobacter sp003852395	77.4325	65	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.47	99.47	0.90	0.90	2	-
GCF_014692875.1	s__Pedobacter sp011759615	77.1915	67	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCF_004331735.1	s__Pedobacter sp004331735	77.0158	54	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331675.1	s__Pedobacter sp004331675	76.7419	50	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205835.1	s__Pedobacter sp014205835	76.6712	62	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215335.1	s__Pedobacter xixiisoli	76.5206	51	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005925345.1	s__Pedobacter ureilyticus	76.4266	50	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755275.1	s__Mucilaginibacter aquatilis	76.3576	59	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196715.1	s__Pedobacter zeae	76.3258	54	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013266735.1	s__Pedobacter foliorum	76.2348	62	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:12,759] [INFO] GTDB search result was written to GCF_022014595.1_ASM2201459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:12,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:12,763] [INFO] DFAST_QC result json was written to GCF_022014595.1_ASM2201459v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:12,763] [INFO] DFAST_QC completed!
[2024-01-24 13:30:12,763] [INFO] Total running time: 0h1m59s