[2024-01-24 13:36:30,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:30,806] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:30,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ad24de3-d2f9-489e-82ca-2f5f1e7822c5/dqc_reference
[2024-01-24 13:36:32,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:32,098] [INFO] Task started: Prodigal
[2024-01-24 13:36:32,098] [INFO] Running command: gunzip -c /var/lib/cwl/stgb89f630f-388b-4426-b64e-7fb50730803e/GCF_005233845.1_ASM523384v1_genomic.fna.gz | prodigal -d GCF_005233845.1_ASM523384v1_genomic.fna/cds.fna -a GCF_005233845.1_ASM523384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:59,638] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:59,639] [INFO] Task started: HMMsearch
[2024-01-24 13:36:59,639] [INFO] Running command: hmmsearch --tblout GCF_005233845.1_ASM523384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ad24de3-d2f9-489e-82ca-2f5f1e7822c5/dqc_reference/reference_markers.hmm GCF_005233845.1_ASM523384v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:59,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:59,971] [INFO] Found 6/6 markers.
[2024-01-24 13:37:00,022] [INFO] Query marker FASTA was written to GCF_005233845.1_ASM523384v1_genomic.fna/markers.fasta
[2024-01-24 13:37:00,023] [INFO] Task started: Blastn
[2024-01-24 13:37:00,023] [INFO] Running command: blastn -query GCF_005233845.1_ASM523384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ad24de3-d2f9-489e-82ca-2f5f1e7822c5/dqc_reference/reference_markers.fasta -out GCF_005233845.1_ASM523384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:00,683] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:00,686] [INFO] Selected 27 target genomes.
[2024-01-24 13:37:00,686] [INFO] Target genome list was writen to GCF_005233845.1_ASM523384v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:00,739] [INFO] Task started: fastANI
[2024-01-24 13:37:00,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89f630f-388b-4426-b64e-7fb50730803e/GCF_005233845.1_ASM523384v1_genomic.fna.gz --refList GCF_005233845.1_ASM523384v1_genomic.fna/target_genomes.txt --output GCF_005233845.1_ASM523384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:23,770] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:23,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ad24de3-d2f9-489e-82ca-2f5f1e7822c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:23,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ad24de3-d2f9-489e-82ca-2f5f1e7822c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:23,784] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:23,784] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:23,785] [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
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	100.0	1921	1926	95	conclusive
Segetibacter koreensis	strain=DSM 18137	GCA_000374045.1	398037	398037	type	True	76.4004	86	1926	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.2561	60	1926	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.2049	66	1926	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.1765	109	1926	95	below_threshold
Segetibacter aerophilus	strain=NBRC 106135	GCA_007991655.1	670293	670293	type	True	76.1745	53	1926	95	below_threshold
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	76.1623	57	1926	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.1555	61	1926	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.1109	118	1926	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	76.0933	142	1926	95	below_threshold
Hanamia caeni	strain=BO-59	GCA_003721595.1	2294116	2294116	type	True	76.0457	64	1926	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.0283	124	1926	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	75.9749	67	1926	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.9338	78	1926	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.8153	119	1926	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	75.5832	72	1926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:23,786] [INFO] DFAST Taxonomy check result was written to GCF_005233845.1_ASM523384v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:23,787] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:23,787] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:23,787] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ad24de3-d2f9-489e-82ca-2f5f1e7822c5/dqc_reference/checkm_data
[2024-01-24 13:37:23,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:23,845] [INFO] Task started: CheckM
[2024-01-24 13:37:23,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005233845.1_ASM523384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005233845.1_ASM523384v1_genomic.fna/checkm_input GCF_005233845.1_ASM523384v1_genomic.fna/checkm_result
[2024-01-24 13:38:38,099] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:38,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:38,121] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:38,121] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:38,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005233845.1_ASM523384v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:38,122] [INFO] Task started: Blastn
[2024-01-24 13:38:38,122] [INFO] Running command: blastn -query GCF_005233845.1_ASM523384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ad24de3-d2f9-489e-82ca-2f5f1e7822c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_005233845.1_ASM523384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:39,132] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:39,141] [INFO] Selected 28 target genomes.
[2024-01-24 13:38:39,141] [INFO] Target genome list was writen to GCF_005233845.1_ASM523384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:39,220] [INFO] Task started: fastANI
[2024-01-24 13:38:39,221] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89f630f-388b-4426-b64e-7fb50730803e/GCF_005233845.1_ASM523384v1_genomic.fna.gz --refList GCF_005233845.1_ASM523384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005233845.1_ASM523384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:58,426] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:58,456] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:58,456] [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_005233845.1	s__Ilyomonas limi	100.0	1921	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ilyomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015999745.1	s__Sediminibacterium sp015999745	76.757	58	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830055.1	s__Lacibacter cauensis	76.5303	71	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013391385.1	s__Sediminibacterium sp013391385	76.2521	65	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306865.1	s__JAFKHH01 sp017306865	76.2363	87	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFKHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361915.1	s__Sediminibacterium goheungense	76.2049	66	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015831355.1	s__Panacibacter sp015831355	76.1765	109	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167075.1	s__Sediminibacterium ginsengisoli	76.1554	61	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115755.1	s__Parafilimonas terrae	76.1538	166	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971225.1	s__Panacibacter ginsenosidivorans	76.1109	118	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097095.1	s__Filimonas sp003097095	76.054	99	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412455.1	s__Deminuibacter soli	76.0283	124	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Deminuibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001623405.1	s__Hydrotalea flava	75.9338	78	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	95.88	95.18	0.90	0.86	13	-
GCA_002399735.1	s__Terrimonas sp002399735	75.8614	62	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013106755.1	s__Panacibacter sp013106755	75.8276	118	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268035.1	s__Parafilimonas sp018268035	75.7641	87	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882935.1	s__JABDFW01 sp903882935	75.7624	72	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JABDFW01	95.0	99.98	99.96	0.98	0.97	5	-
GCA_003963365.1	s__AWTP1-9 sp003963365	75.6794	82	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379905.1	s__Ferruginibacter sp014379905	75.4915	57	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478885.1	s__Panacibacter sp002478885	75.2943	84	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	99.95	99.95	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:58,458] [INFO] GTDB search result was written to GCF_005233845.1_ASM523384v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:58,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:58,466] [INFO] DFAST_QC result json was written to GCF_005233845.1_ASM523384v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:58,466] [INFO] DFAST_QC completed!
[2024-01-24 13:38:58,466] [INFO] Total running time: 0h2m28s