[2024-01-24 13:28:25,826] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cfc6492-9311-41fe-a221-c9bdd01f98ed/dqc_reference
[2024-01-24 13:28:27,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:27,177] [INFO] Task started: Prodigal
[2024-01-24 13:28:27,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg77610209-6e1f-42c1-961b-0fc3e587acb4/GCF_008086205.1_ASM808620v1_genomic.fna.gz | prodigal -d GCF_008086205.1_ASM808620v1_genomic.fna/cds.fna -a GCF_008086205.1_ASM808620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:38,822] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:38,823] [INFO] Task started: HMMsearch
[2024-01-24 13:28:38,823] [INFO] Running command: hmmsearch --tblout GCF_008086205.1_ASM808620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cfc6492-9311-41fe-a221-c9bdd01f98ed/dqc_reference/reference_markers.hmm GCF_008086205.1_ASM808620v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:39,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:39,144] [INFO] Found 6/6 markers.
[2024-01-24 13:28:39,181] [INFO] Query marker FASTA was written to GCF_008086205.1_ASM808620v1_genomic.fna/markers.fasta
[2024-01-24 13:28:39,182] [INFO] Task started: Blastn
[2024-01-24 13:28:39,182] [INFO] Running command: blastn -query GCF_008086205.1_ASM808620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cfc6492-9311-41fe-a221-c9bdd01f98ed/dqc_reference/reference_markers.fasta -out GCF_008086205.1_ASM808620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:39,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:39,881] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:39,881] [INFO] Target genome list was writen to GCF_008086205.1_ASM808620v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:39,890] [INFO] Task started: fastANI
[2024-01-24 13:28:39,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg77610209-6e1f-42c1-961b-0fc3e587acb4/GCF_008086205.1_ASM808620v1_genomic.fna.gz --refList GCF_008086205.1_ASM808620v1_genomic.fna/target_genomes.txt --output GCF_008086205.1_ASM808620v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:49,786] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:49,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cfc6492-9311-41fe-a221-c9bdd01f98ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:49,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cfc6492-9311-41fe-a221-c9bdd01f98ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:49,799] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:49,799] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:49,799] [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
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	100.0	1111	1112	95	conclusive
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	82.1719	722	1112	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	81.6171	738	1112	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	80.5843	644	1112	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	78.2465	316	1112	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	78.1446	293	1112	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	78.0975	307	1112	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	78.0234	265	1112	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.8223	314	1112	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7158	235	1112	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	77.698	233	1112	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.6408	245	1112	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.6372	248	1112	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3235	209	1112	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.1814	212	1112	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:49,801] [INFO] DFAST Taxonomy check result was written to GCF_008086205.1_ASM808620v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:49,801] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:49,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:49,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cfc6492-9311-41fe-a221-c9bdd01f98ed/dqc_reference/checkm_data
[2024-01-24 13:28:49,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:49,838] [INFO] Task started: CheckM
[2024-01-24 13:28:49,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008086205.1_ASM808620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008086205.1_ASM808620v1_genomic.fna/checkm_input GCF_008086205.1_ASM808620v1_genomic.fna/checkm_result
[2024-01-24 13:29:27,162] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:27,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:27,188] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:27,189] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:27,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008086205.1_ASM808620v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:27,190] [INFO] Task started: Blastn
[2024-01-24 13:29:27,190] [INFO] Running command: blastn -query GCF_008086205.1_ASM808620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cfc6492-9311-41fe-a221-c9bdd01f98ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_008086205.1_ASM808620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:28,116] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:28,131] [INFO] Selected 12 target genomes.
[2024-01-24 13:29:28,131] [INFO] Target genome list was writen to GCF_008086205.1_ASM808620v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:28,150] [INFO] Task started: fastANI
[2024-01-24 13:29:28,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg77610209-6e1f-42c1-961b-0fc3e587acb4/GCF_008086205.1_ASM808620v1_genomic.fna.gz --refList GCF_008086205.1_ASM808620v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008086205.1_ASM808620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:36,748] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:36,766] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:36,766] [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_008086205.1	s__Algorimicrobium myxarmorum	100.0	1112	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000224335.1	s__Algorimicrobium argentinense	82.1565	723	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	81.638	737	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002414705.1	s__Algorimicrobium sp002414705	80.8287	619	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115185.1	s__Algorimicrobium echini	80.6358	645	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCF_012931685.1	s__Pseudobizionia ponticola	78.2344	317	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCF_008084905.1	s__Xanthomarina maritima	78.1095	334	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	77.8557	315	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.7901	231	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_900112595.1	s__Algibacter_B pectinivorans	77.7008	232	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.6915	236	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	77.6034	268	1112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:36,768] [INFO] GTDB search result was written to GCF_008086205.1_ASM808620v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:36,768] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:36,772] [INFO] DFAST_QC result json was written to GCF_008086205.1_ASM808620v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:36,772] [INFO] DFAST_QC completed!
[2024-01-24 13:29:36,772] [INFO] Total running time: 0h1m11s