[2024-01-24 13:32:11,934] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:11,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:11,938] [INFO] DQC Reference Directory: /var/lib/cwl/stgafd0bcac-13f9-4e1d-a8c8-631eca831951/dqc_reference
[2024-01-24 13:32:14,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:14,741] [INFO] Task started: Prodigal
[2024-01-24 13:32:14,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg85f409ec-787a-4506-9d13-497af96e675d/GCF_007997225.1_ASM799722v1_genomic.fna.gz | prodigal -d GCF_007997225.1_ASM799722v1_genomic.fna/cds.fna -a GCF_007997225.1_ASM799722v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:37,426] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:37,427] [INFO] Task started: HMMsearch
[2024-01-24 13:32:37,427] [INFO] Running command: hmmsearch --tblout GCF_007997225.1_ASM799722v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafd0bcac-13f9-4e1d-a8c8-631eca831951/dqc_reference/reference_markers.hmm GCF_007997225.1_ASM799722v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:37,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:37,728] [INFO] Found 6/6 markers.
[2024-01-24 13:32:37,769] [INFO] Query marker FASTA was written to GCF_007997225.1_ASM799722v1_genomic.fna/markers.fasta
[2024-01-24 13:32:37,770] [INFO] Task started: Blastn
[2024-01-24 13:32:37,770] [INFO] Running command: blastn -query GCF_007997225.1_ASM799722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd0bcac-13f9-4e1d-a8c8-631eca831951/dqc_reference/reference_markers.fasta -out GCF_007997225.1_ASM799722v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:38,433] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:38,446] [INFO] Selected 26 target genomes.
[2024-01-24 13:32:38,446] [INFO] Target genome list was writen to GCF_007997225.1_ASM799722v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:38,474] [INFO] Task started: fastANI
[2024-01-24 13:32:38,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg85f409ec-787a-4506-9d13-497af96e675d/GCF_007997225.1_ASM799722v1_genomic.fna.gz --refList GCF_007997225.1_ASM799722v1_genomic.fna/target_genomes.txt --output GCF_007997225.1_ASM799722v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:55,317] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:55,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafd0bcac-13f9-4e1d-a8c8-631eca831951/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:55,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafd0bcac-13f9-4e1d-a8c8-631eca831951/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:55,340] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:55,340] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:55,341] [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
Subsaximicrobium wynnwilliamsii	strain=G#7(T)	GCA_007997225.1	291179	291179	type	True	100.0	1572	1575	95	conclusive
Gelidibacter algens	strain=ACAM 536	GCA_001678675.1	49280	49280	type	True	79.471	306	1575	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	79.2821	306	1575	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	77.4415	159	1575	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.4023	160	1575	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.1812	170	1575	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.1049	186	1575	95	below_threshold
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	77.0283	207	1575	95	below_threshold
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	77.0145	168	1575	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	76.9561	180	1575	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.8479	104	1575	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.8262	101	1575	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.8039	148	1575	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.7547	74	1575	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6763	104	1575	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.643	91	1575	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	76.6319	110	1575	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.4834	116	1575	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.466	114	1575	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	76.46	117	1575	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	76.4576	123	1575	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	76.4491	115	1575	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.4463	117	1575	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.4232	96	1575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:55,343] [INFO] DFAST Taxonomy check result was written to GCF_007997225.1_ASM799722v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:55,344] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:55,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:55,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafd0bcac-13f9-4e1d-a8c8-631eca831951/dqc_reference/checkm_data
[2024-01-24 13:32:55,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:55,391] [INFO] Task started: CheckM
[2024-01-24 13:32:55,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007997225.1_ASM799722v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007997225.1_ASM799722v1_genomic.fna/checkm_input GCF_007997225.1_ASM799722v1_genomic.fna/checkm_result
[2024-01-24 13:34:00,431] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:00,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:00,559] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:00,560] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:00,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007997225.1_ASM799722v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:00,561] [INFO] Task started: Blastn
[2024-01-24 13:34:00,561] [INFO] Running command: blastn -query GCF_007997225.1_ASM799722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd0bcac-13f9-4e1d-a8c8-631eca831951/dqc_reference/reference_markers_gtdb.fasta -out GCF_007997225.1_ASM799722v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:01,515] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:01,521] [INFO] Selected 21 target genomes.
[2024-01-24 13:34:01,521] [INFO] Target genome list was writen to GCF_007997225.1_ASM799722v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:01,540] [INFO] Task started: fastANI
[2024-01-24 13:34:01,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg85f409ec-787a-4506-9d13-497af96e675d/GCF_007997225.1_ASM799722v1_genomic.fna.gz --refList GCF_007997225.1_ASM799722v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007997225.1_ASM799722v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:16,456] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:16,475] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:16,476] [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_007997225.1	s__Subsaximicrobium wynnwilliamsii	100.0	1572	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Subsaximicrobium	95.0	100.00	99.99	0.99	0.99	3	conclusive
GCF_000688335.1	s__Subsaximicrobium sp000688335	77.4956	285	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Subsaximicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799465.1	s__Psychroserpens sp000799465	77.4625	267	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364975.1	s__Gelidibacter sediminis	77.4059	159	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016469035.1	s__Gelidibacter salicanalis_A	77.2958	199	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	77.2851	228	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	77.2515	178	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	77.1812	170	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	77.108	202	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	77.0693	127	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004115975.1	s__Gelidibacter gilvus	77.0398	206	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997285.1	s__Gelidibacter salicanalis	76.9997	169	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012931685.1	s__Pseudobizionia ponticola	76.9453	101	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCA_018222875.1	s__Psychroserpens sp018222875	76.8743	161	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	76.864	103	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCA_002426755.1	s__Aquaticitalea sp002426755	76.8614	183	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	76.8262	101	1575	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_013404085.1	s__Winogradskyella helgolandensis	76.7901	149	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCA_905479815.1	s__Psychroserpens sp905479815	76.6878	147	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843175.1	s__Confluentibacter flavum	76.5615	112	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	76.4463	117	1575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:16,477] [INFO] GTDB search result was written to GCF_007997225.1_ASM799722v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:16,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:16,483] [INFO] DFAST_QC result json was written to GCF_007997225.1_ASM799722v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:16,484] [INFO] DFAST_QC completed!
[2024-01-24 13:34:16,484] [INFO] Total running time: 0h2m5s