[2024-01-25 18:06:35,696] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:35,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:35,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgd65ea88b-3d0f-4910-8cfd-695eddbae4df/dqc_reference
[2024-01-25 18:06:36,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:36,895] [INFO] Task started: Prodigal
[2024-01-25 18:06:36,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg8361cbd9-b546-43e4-9eb2-650a8a74d69d/GCF_014636995.1_ASM1463699v1_genomic.fna.gz | prodigal -d GCF_014636995.1_ASM1463699v1_genomic.fna/cds.fna -a GCF_014636995.1_ASM1463699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:45,905] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:45,905] [INFO] Task started: HMMsearch
[2024-01-25 18:06:45,905] [INFO] Running command: hmmsearch --tblout GCF_014636995.1_ASM1463699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd65ea88b-3d0f-4910-8cfd-695eddbae4df/dqc_reference/reference_markers.hmm GCF_014636995.1_ASM1463699v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:46,119] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:46,120] [INFO] Found 6/6 markers.
[2024-01-25 18:06:46,148] [INFO] Query marker FASTA was written to GCF_014636995.1_ASM1463699v1_genomic.fna/markers.fasta
[2024-01-25 18:06:46,148] [INFO] Task started: Blastn
[2024-01-25 18:06:46,148] [INFO] Running command: blastn -query GCF_014636995.1_ASM1463699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65ea88b-3d0f-4910-8cfd-695eddbae4df/dqc_reference/reference_markers.fasta -out GCF_014636995.1_ASM1463699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:46,763] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:46,765] [INFO] Selected 17 target genomes.
[2024-01-25 18:06:46,766] [INFO] Target genome list was writen to GCF_014636995.1_ASM1463699v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:46,775] [INFO] Task started: fastANI
[2024-01-25 18:06:46,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg8361cbd9-b546-43e4-9eb2-650a8a74d69d/GCF_014636995.1_ASM1463699v1_genomic.fna.gz --refList GCF_014636995.1_ASM1463699v1_genomic.fna/target_genomes.txt --output GCF_014636995.1_ASM1463699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:57,336] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:57,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd65ea88b-3d0f-4910-8cfd-695eddbae4df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:57,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd65ea88b-3d0f-4910-8cfd-695eddbae4df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:57,346] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:06:57,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:57,346] [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
Mangrovimonas yunxiaonensis	strain=CGMCC 1.12280	GCA_014636995.1	1197477	1197477	type	True	100.0	872	872	95	conclusive
Mangrovimonas yunxiaonensis	strain=LY01	GCA_000733475.1	1197477	1197477	type	True	99.9934	870	872	95	conclusive
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	80.6355	489	872	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	78.5435	162	872	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.793	213	872	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.3543	266	872	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.2532	153	872	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.1871	131	872	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	77.142	171	872	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.107	160	872	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	77.0819	182	872	95	below_threshold
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	77.0585	159	872	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.9599	137	872	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.8606	168	872	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.7289	121	872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:57,347] [INFO] DFAST Taxonomy check result was written to GCF_014636995.1_ASM1463699v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:57,348] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:57,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:57,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd65ea88b-3d0f-4910-8cfd-695eddbae4df/dqc_reference/checkm_data
[2024-01-25 18:06:57,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:57,377] [INFO] Task started: CheckM
[2024-01-25 18:06:57,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636995.1_ASM1463699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636995.1_ASM1463699v1_genomic.fna/checkm_input GCF_014636995.1_ASM1463699v1_genomic.fna/checkm_result
[2024-01-25 18:07:25,581] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:25,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:25,606] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:25,607] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:25,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636995.1_ASM1463699v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:25,607] [INFO] Task started: Blastn
[2024-01-25 18:07:25,607] [INFO] Running command: blastn -query GCF_014636995.1_ASM1463699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65ea88b-3d0f-4910-8cfd-695eddbae4df/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636995.1_ASM1463699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:26,558] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:26,561] [INFO] Selected 18 target genomes.
[2024-01-25 18:07:26,561] [INFO] Target genome list was writen to GCF_014636995.1_ASM1463699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:26,586] [INFO] Task started: fastANI
[2024-01-25 18:07:26,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg8361cbd9-b546-43e4-9eb2-650a8a74d69d/GCF_014636995.1_ASM1463699v1_genomic.fna.gz --refList GCF_014636995.1_ASM1463699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636995.1_ASM1463699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:37,283] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:37,294] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:37,295] [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_000733475.1	s__Mangrovimonas yunxiaonensis	99.9934	870	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	98.99	97.98	0.98	0.97	3	conclusive
GCF_003944795.1	s__Mangrovimonas spongiae	80.6257	490	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	78.54	161	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	78.1603	185	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_004366715.1	s__Meridianimaribacter flavus	78.1235	237	872	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	77.6855	196	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002225.1	s__Winogradskyella sp013002225	77.3886	82	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348685.1	s__Xanthomarina gelatinilytica	77.3433	267	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	98.37	98.31	0.90	0.88	4	-
GCF_004346845.1	s__Winogradskyella wandonensis	77.1835	132	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685485.1	s__Formosa haliotis	77.0967	174	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943555.1	s__Tamlana_B nanhaiensis	77.0902	183	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943565.1	s__Tamlana_B sedimentorum	77.0585	159	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893765.1	s__Tamlana_A carrageenivorans	77.0547	146	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364975.1	s__Gelidibacter sediminis	77.0113	111	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129745.1	s__Winogradskyella jejuensis	76.9549	117	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	76.8958	121	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCF_008086205.1	s__Algorimicrobium myxarmorum	76.8462	169	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	76.7289	121	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:37,296] [INFO] GTDB search result was written to GCF_014636995.1_ASM1463699v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:37,296] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:37,301] [INFO] DFAST_QC result json was written to GCF_014636995.1_ASM1463699v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:37,301] [INFO] DFAST_QC completed!
[2024-01-25 18:07:37,301] [INFO] Total running time: 0h1m2s