[2024-01-24 12:52:26,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:26,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:26,812] [INFO] DQC Reference Directory: /var/lib/cwl/stgae290077-030b-4ad8-aecb-5eee39c6d3d9/dqc_reference
[2024-01-24 12:52:28,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:28,085] [INFO] Task started: Prodigal
[2024-01-24 12:52:28,085] [INFO] Running command: gunzip -c /var/lib/cwl/stgd772f4e1-f1e8-4fd1-b498-4995def6e74d/GCF_014641635.1_ASM1464163v1_genomic.fna.gz | prodigal -d GCF_014641635.1_ASM1464163v1_genomic.fna/cds.fna -a GCF_014641635.1_ASM1464163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:37,476] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:37,477] [INFO] Task started: HMMsearch
[2024-01-24 12:52:37,477] [INFO] Running command: hmmsearch --tblout GCF_014641635.1_ASM1464163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae290077-030b-4ad8-aecb-5eee39c6d3d9/dqc_reference/reference_markers.hmm GCF_014641635.1_ASM1464163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:37,741] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:37,743] [INFO] Found 6/6 markers.
[2024-01-24 12:52:37,772] [INFO] Query marker FASTA was written to GCF_014641635.1_ASM1464163v1_genomic.fna/markers.fasta
[2024-01-24 12:52:37,773] [INFO] Task started: Blastn
[2024-01-24 12:52:37,773] [INFO] Running command: blastn -query GCF_014641635.1_ASM1464163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae290077-030b-4ad8-aecb-5eee39c6d3d9/dqc_reference/reference_markers.fasta -out GCF_014641635.1_ASM1464163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:38,478] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:38,481] [INFO] Selected 28 target genomes.
[2024-01-24 12:52:38,481] [INFO] Target genome list was writen to GCF_014641635.1_ASM1464163v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:38,498] [INFO] Task started: fastANI
[2024-01-24 12:52:38,498] [INFO] Running command: fastANI --query /var/lib/cwl/stgd772f4e1-f1e8-4fd1-b498-4995def6e74d/GCF_014641635.1_ASM1464163v1_genomic.fna.gz --refList GCF_014641635.1_ASM1464163v1_genomic.fna/target_genomes.txt --output GCF_014641635.1_ASM1464163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:56,707] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:56,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae290077-030b-4ad8-aecb-5eee39c6d3d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:56,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae290077-030b-4ad8-aecb-5eee39c6d3d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:56,734] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:52:56,735] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:52:56,735] [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
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	78.4029	370	1030	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	78.2165	353	1030	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	78.0625	288	1030	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	78.0062	310	1030	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.9324	357	1030	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.9091	282	1030	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	77.8909	302	1030	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.8904	253	1030	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.8889	276	1030	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.8506	257	1030	95	below_threshold
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	77.8179	230	1030	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.8101	333	1030	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.7163	298	1030	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	77.6353	292	1030	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.6353	292	1030	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.6327	292	1030	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.6204	192	1030	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	77.5902	237	1030	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	77.5798	274	1030	95	below_threshold
Gelidibacter japonicus	strain=Bio7-1	GCA_010725055.1	1962232	1962232	type	True	77.5549	234	1030	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.4861	234	1030	95	below_threshold
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	77.4683	246	1030	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	77.4188	302	1030	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.3891	237	1030	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	77.3411	233	1030	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	77.3339	236	1030	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.3284	263	1030	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2583	204	1030	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:56,737] [INFO] DFAST Taxonomy check result was written to GCF_014641635.1_ASM1464163v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:56,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:56,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:56,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae290077-030b-4ad8-aecb-5eee39c6d3d9/dqc_reference/checkm_data
[2024-01-24 12:52:56,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:56,772] [INFO] Task started: CheckM
[2024-01-24 12:52:56,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641635.1_ASM1464163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641635.1_ASM1464163v1_genomic.fna/checkm_input GCF_014641635.1_ASM1464163v1_genomic.fna/checkm_result
[2024-01-24 12:53:28,773] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:28,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:28,799] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:28,800] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:28,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641635.1_ASM1464163v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:28,801] [INFO] Task started: Blastn
[2024-01-24 12:53:28,801] [INFO] Running command: blastn -query GCF_014641635.1_ASM1464163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae290077-030b-4ad8-aecb-5eee39c6d3d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641635.1_ASM1464163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:29,765] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:29,769] [INFO] Selected 17 target genomes.
[2024-01-24 12:53:29,770] [INFO] Target genome list was writen to GCF_014641635.1_ASM1464163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:29,844] [INFO] Task started: fastANI
[2024-01-24 12:53:29,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgd772f4e1-f1e8-4fd1-b498-4995def6e74d/GCF_014641635.1_ASM1464163v1_genomic.fna.gz --refList GCF_014641635.1_ASM1464163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641635.1_ASM1464163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:41,026] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:41,042] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:41,042] [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_014641635.1	s__Aquaticitalea lipolytica	100.0	1030	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002426015.1	s__Aquaticitalea sp002426015	83.5657	604	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	79.0327	462	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	78.875	443	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_008084905.1	s__Xanthomarina maritima	78.6099	350	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	78.4029	370	1030	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	78.3671	400	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.3199	395	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426755.1	s__Aquaticitalea sp002426755	78.3068	351	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	78.2203	342	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	77.9921	319	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764305.1	s__Mesoflavibacter profundi	77.9724	338	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_000799465.1	s__Psychroserpens sp000799465	77.9364	302	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	77.9267	315	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414705.1	s__Algorimicrobium sp002414705	77.9012	282	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	77.7238	336	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	77.5367	294	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:41,045] [INFO] GTDB search result was written to GCF_014641635.1_ASM1464163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:41,046] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:41,056] [INFO] DFAST_QC result json was written to GCF_014641635.1_ASM1464163v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:41,056] [INFO] DFAST_QC completed!
[2024-01-24 12:53:41,056] [INFO] Total running time: 0h1m14s