[2023-03-17 07:44:38,122] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:38,123] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:38,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ebba40b-43c1-4a42-b0a5-e786e3977289/dqc_reference
[2023-03-17 07:44:43,313] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:43,314] [INFO] Task started: Prodigal
[2023-03-17 07:44:43,315] [INFO] Running command: cat /var/lib/cwl/stg6f54e67b-d19d-4ec3-bb1d-85cd85c3b18a/OceanDNA-b7157.fa | prodigal -d OceanDNA-b7157/cds.fna -a OceanDNA-b7157/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:44:58,055] [INFO] Task succeeded: Prodigal
[2023-03-17 07:44:58,056] [INFO] Task started: HMMsearch
[2023-03-17 07:44:58,056] [INFO] Running command: hmmsearch --tblout OceanDNA-b7157/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ebba40b-43c1-4a42-b0a5-e786e3977289/dqc_reference/reference_markers.hmm OceanDNA-b7157/protein.faa > /dev/null
[2023-03-17 07:44:58,274] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:44:58,275] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6f54e67b-d19d-4ec3-bb1d-85cd85c3b18a/OceanDNA-b7157.fa]
[2023-03-17 07:44:58,288] [INFO] Query marker FASTA was written to OceanDNA-b7157/markers.fasta
[2023-03-17 07:44:58,290] [INFO] Task started: Blastn
[2023-03-17 07:44:58,290] [INFO] Running command: blastn -query OceanDNA-b7157/markers.fasta -db /var/lib/cwl/stg1ebba40b-43c1-4a42-b0a5-e786e3977289/dqc_reference/reference_markers.fasta -out OceanDNA-b7157/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:01,621] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:01,622] [INFO] Selected 24 target genomes.
[2023-03-17 07:45:01,622] [INFO] Target genome list was writen to OceanDNA-b7157/target_genomes.txt
[2023-03-17 07:45:01,635] [INFO] Task started: fastANI
[2023-03-17 07:45:01,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f54e67b-d19d-4ec3-bb1d-85cd85c3b18a/OceanDNA-b7157.fa --refList OceanDNA-b7157/target_genomes.txt --output OceanDNA-b7157/fastani_result.tsv --threads 1
[2023-03-17 07:45:16,198] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:16,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ebba40b-43c1-4a42-b0a5-e786e3977289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:45:16,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ebba40b-43c1-4a42-b0a5-e786e3977289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:45:16,219] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:45:16,219] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:45:16,219] [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
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	77.6925	157	688	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	77.563	214	688	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	77.5237	193	688	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.5233	202	688	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	77.5039	229	688	95	below_threshold
Gelidibacter algens	strain=ACAM 536	GCA_001678675.1	49280	49280	type	True	77.4965	222	688	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	77.4545	212	688	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	77.4318	173	688	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.4286	222	688	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	77.4229	167	688	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	77.346	182	688	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	77.292	205	688	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.169	156	688	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	77.1409	144	688	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	77.0566	143	688	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	77.0369	150	688	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	76.9956	138	688	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.9933	194	688	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.7787	134	688	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.7657	116	688	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.7305	139	688	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	76.615	119	688	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.6034	120	688	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.4695	76	688	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:45:16,219] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7157/tc_result.tsv
[2023-03-17 07:45:16,219] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:45:16,219] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:45:16,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ebba40b-43c1-4a42-b0a5-e786e3977289/dqc_reference/checkm_data
[2023-03-17 07:45:16,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:45:16,224] [INFO] Task started: CheckM
[2023-03-17 07:45:16,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7157/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7157/checkm_input OceanDNA-b7157/checkm_result
[2023-03-17 07:45:58,751] [INFO] Task succeeded: CheckM
[2023-03-17 07:45:58,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:45:58,754] [INFO] ===== Completeness check finished =====
[2023-03-17 07:45:58,754] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:45:58,754] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7157/markers.fasta)
[2023-03-17 07:45:58,755] [INFO] Task started: Blastn
[2023-03-17 07:45:58,755] [INFO] Running command: blastn -query OceanDNA-b7157/markers.fasta -db /var/lib/cwl/stg1ebba40b-43c1-4a42-b0a5-e786e3977289/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7157/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:59,748] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:59,749] [INFO] Selected 25 target genomes.
[2023-03-17 07:45:59,749] [INFO] Target genome list was writen to OceanDNA-b7157/target_genomes_gtdb.txt
[2023-03-17 07:45:59,902] [INFO] Task started: fastANI
[2023-03-17 07:45:59,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f54e67b-d19d-4ec3-bb1d-85cd85c3b18a/OceanDNA-b7157.fa --refList OceanDNA-b7157/target_genomes_gtdb.txt --output OceanDNA-b7157/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:46:14,236] [INFO] Task succeeded: fastANI
[2023-03-17 07:46:14,250] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:46:14,250] [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	78.309	322	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426015.1	s__Aquaticitalea sp002426015	78.0836	301	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.9212	255	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_002807055.1	s__Confluentibacter citreus	77.6925	157	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.6879	238	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364975.1	s__Gelidibacter sediminis	77.5687	212	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	77.5237	193	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	77.5233	202	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678675.1	s__Gelidibacter algens	77.4965	222	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	99.95	99.95	0.98	0.98	2	-
GCF_017814435.1	s__Mariniflexile gromovii	77.4869	209	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826645.1	s__Psychroserpens mesophilus	77.4692	219	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	77.4551	170	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843175.1	s__Confluentibacter flavum	77.4245	166	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806995.1	s__Confluentibacter lentus	77.347	181	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104785.1	s__Psychroserpens sp900104785	77.2817	166	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722255.1	s__Winogradskyella sp002722255	77.2083	130	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCA_018222875.1	s__Psychroserpens sp018222875	77.1916	194	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685485.1	s__Formosa haliotis	77.153	141	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	77.0649	160	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_014243395.1	s__Winogradskyella flava	77.0384	144	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869935.1	s__Winogradskyella algicola	77.0375	148	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971725.1	s__Winogradskyella sp001971725	76.9215	140	688	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	76.8709	153	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_000425645.1	s__Gaetbulibacter saemankumensis	76.6227	119	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154725.1	s__Kordia algicida	76.6091	118	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:46:14,250] [INFO] GTDB search result was written to OceanDNA-b7157/result_gtdb.tsv
[2023-03-17 07:46:14,250] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:46:14,253] [INFO] DFAST_QC result json was written to OceanDNA-b7157/dqc_result.json
[2023-03-17 07:46:14,253] [INFO] DFAST_QC completed!
[2023-03-17 07:46:14,253] [INFO] Total running time: 0h1m36s