[2024-01-24 12:39:40,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:40,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:40,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg63a6586c-1570-4815-8b22-b85cb45dff6a/dqc_reference
[2024-01-24 12:39:42,313] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:42,314] [INFO] Task started: Prodigal
[2024-01-24 12:39:42,314] [INFO] Running command: gunzip -c /var/lib/cwl/stga3d71a4e-4de3-41ca-a56d-a76be2c505c7/GCF_025244665.1_ASM2524466v1_genomic.fna.gz | prodigal -d GCF_025244665.1_ASM2524466v1_genomic.fna/cds.fna -a GCF_025244665.1_ASM2524466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:01,680] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:01,681] [INFO] Task started: HMMsearch
[2024-01-24 12:40:01,681] [INFO] Running command: hmmsearch --tblout GCF_025244665.1_ASM2524466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63a6586c-1570-4815-8b22-b85cb45dff6a/dqc_reference/reference_markers.hmm GCF_025244665.1_ASM2524466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:02,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:02,033] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga3d71a4e-4de3-41ca-a56d-a76be2c505c7/GCF_025244665.1_ASM2524466v1_genomic.fna.gz]
[2024-01-24 12:40:02,089] [INFO] Query marker FASTA was written to GCF_025244665.1_ASM2524466v1_genomic.fna/markers.fasta
[2024-01-24 12:40:02,090] [INFO] Task started: Blastn
[2024-01-24 12:40:02,091] [INFO] Running command: blastn -query GCF_025244665.1_ASM2524466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63a6586c-1570-4815-8b22-b85cb45dff6a/dqc_reference/reference_markers.fasta -out GCF_025244665.1_ASM2524466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:02,747] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:02,751] [INFO] Selected 19 target genomes.
[2024-01-24 12:40:02,751] [INFO] Target genome list was writen to GCF_025244665.1_ASM2524466v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:02,771] [INFO] Task started: fastANI
[2024-01-24 12:40:02,772] [INFO] Running command: fastANI --query /var/lib/cwl/stga3d71a4e-4de3-41ca-a56d-a76be2c505c7/GCF_025244665.1_ASM2524466v1_genomic.fna.gz --refList GCF_025244665.1_ASM2524466v1_genomic.fna/target_genomes.txt --output GCF_025244665.1_ASM2524466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:17,182] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:17,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63a6586c-1570-4815-8b22-b85cb45dff6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:17,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63a6586c-1570-4815-8b22-b85cb45dff6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:17,196] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:17,196] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:17,196] [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
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	81.7119	841	1288	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	81.6284	817	1288	95	below_threshold
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	80.7735	771	1288	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	79.768	678	1288	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	79.7552	683	1288	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	77.9436	317	1288	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	77.2717	236	1288	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	76.9462	201	1288	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	76.8482	95	1288	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	76.8344	134	1288	95	below_threshold
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	76.7802	86	1288	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	76.7346	85	1288	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.6795	116	1288	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.5182	124	1288	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.4529	146	1288	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.4143	147	1288	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	76.3857	119	1288	95	below_threshold
Pricia antarctica	strain=DSM 23421	GCA_900101815.1	641691	641691	type	True	76.219	93	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:17,198] [INFO] DFAST Taxonomy check result was written to GCF_025244665.1_ASM2524466v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:17,198] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:17,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:17,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63a6586c-1570-4815-8b22-b85cb45dff6a/dqc_reference/checkm_data
[2024-01-24 12:40:17,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:17,239] [INFO] Task started: CheckM
[2024-01-24 12:40:17,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025244665.1_ASM2524466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025244665.1_ASM2524466v1_genomic.fna/checkm_input GCF_025244665.1_ASM2524466v1_genomic.fna/checkm_result
[2024-01-24 12:41:11,100] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:11,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:11,125] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:11,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:11,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025244665.1_ASM2524466v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:11,126] [INFO] Task started: Blastn
[2024-01-24 12:41:11,126] [INFO] Running command: blastn -query GCF_025244665.1_ASM2524466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63a6586c-1570-4815-8b22-b85cb45dff6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_025244665.1_ASM2524466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:11,912] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:11,917] [INFO] Selected 22 target genomes.
[2024-01-24 12:41:11,917] [INFO] Target genome list was writen to GCF_025244665.1_ASM2524466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:11,954] [INFO] Task started: fastANI
[2024-01-24 12:41:11,954] [INFO] Running command: fastANI --query /var/lib/cwl/stga3d71a4e-4de3-41ca-a56d-a76be2c505c7/GCF_025244665.1_ASM2524466v1_genomic.fna.gz --refList GCF_025244665.1_ASM2524466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025244665.1_ASM2524466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:26,944] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:26,960] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:41:26,960] [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_008386635.1	s__Maribacter flavus	81.7216	841	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_003933245.1	s__Maribacter algicola	80.7735	771	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742265.1	s__Maribacter sp002742265	80.3373	752	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269385.1	s__Maribacter cobaltidurans	79.7731	685	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001020565.1	s__Maribacter thermophilus	77.9607	317	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100785.1	s__Maribacter sp018100785	77.789	320	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970695.1	s__Maribacter sp002742365	77.6777	223	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_900188415.1	s__Maribacter sedimenticola	77.26	237	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_005144745.1	s__Croceivirga sp005144745	77.1398	82	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.80	97.80	0.93	0.93	2	-
GCA_011050675.1	s__Maribacter sp011050675	77.0003	167	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900109345.1	s__Maribacter orientalis	76.9462	201	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235875.1	s__Croceivirga lutea	76.7802	86	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001306415.1	s__Croceitalea dokdonensis	76.7482	110	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883545.1	s__Confluentibacter sp018883545	76.7473	53	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885635.1	s__RZ26 sp005885635	76.6795	116	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	76.4529	146	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_003382275.1	s__Muricauda nanhaiensis	76.3857	119	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683825.1	s__Zeaxanthinibacter sp001683825	76.2442	70	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:26,963] [INFO] GTDB search result was written to GCF_025244665.1_ASM2524466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:26,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:26,968] [INFO] DFAST_QC result json was written to GCF_025244665.1_ASM2524466v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:26,968] [INFO] DFAST_QC completed!
[2024-01-24 12:41:26,969] [INFO] Total running time: 0h1m46s