[2023-03-16 17:42:49,561] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:42:49,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:42:49,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg1de66833-071f-4d1b-9b6b-d7b6c86c0e6e/dqc_reference
[2023-03-16 17:42:52,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:42:52,304] [INFO] Task started: Prodigal
[2023-03-16 17:42:52,305] [INFO] Running command: cat /var/lib/cwl/stg9ae88f45-5f48-472c-b0a9-59215262c3c6/OceanDNA-b7699.fa | prodigal -d OceanDNA-b7699/cds.fna -a OceanDNA-b7699/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:43:01,595] [INFO] Task succeeded: Prodigal
[2023-03-16 17:43:01,595] [INFO] Task started: HMMsearch
[2023-03-16 17:43:01,595] [INFO] Running command: hmmsearch --tblout OceanDNA-b7699/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1de66833-071f-4d1b-9b6b-d7b6c86c0e6e/dqc_reference/reference_markers.hmm OceanDNA-b7699/protein.faa > /dev/null
[2023-03-16 17:43:01,780] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:43:01,781] [INFO] Found 6/6 markers.
[2023-03-16 17:43:01,793] [INFO] Query marker FASTA was written to OceanDNA-b7699/markers.fasta
[2023-03-16 17:43:01,794] [INFO] Task started: Blastn
[2023-03-16 17:43:01,795] [INFO] Running command: blastn -query OceanDNA-b7699/markers.fasta -db /var/lib/cwl/stg1de66833-071f-4d1b-9b6b-d7b6c86c0e6e/dqc_reference/reference_markers.fasta -out OceanDNA-b7699/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:43:02,352] [INFO] Task succeeded: Blastn
[2023-03-16 17:43:02,353] [INFO] Selected 28 target genomes.
[2023-03-16 17:43:02,353] [INFO] Target genome list was writen to OceanDNA-b7699/target_genomes.txt
[2023-03-16 17:43:02,395] [INFO] Task started: fastANI
[2023-03-16 17:43:02,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae88f45-5f48-472c-b0a9-59215262c3c6/OceanDNA-b7699.fa --refList OceanDNA-b7699/target_genomes.txt --output OceanDNA-b7699/fastani_result.tsv --threads 1
[2023-03-16 17:43:18,356] [INFO] Task succeeded: fastANI
[2023-03-16 17:43:18,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1de66833-071f-4d1b-9b6b-d7b6c86c0e6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:43:18,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1de66833-071f-4d1b-9b6b-d7b6c86c0e6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:43:18,364] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:43:18,365] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:43:18,365] [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
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	75.7801	58	471	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.55	69	471	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	75.4929	51	471	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	75.4924	51	471	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	75.3514	56	471	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:43:18,365] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7699/tc_result.tsv
[2023-03-16 17:43:18,365] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:43:18,365] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:43:18,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1de66833-071f-4d1b-9b6b-d7b6c86c0e6e/dqc_reference/checkm_data
[2023-03-16 17:43:18,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:43:18,381] [INFO] Task started: CheckM
[2023-03-16 17:43:18,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7699/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7699/checkm_input OceanDNA-b7699/checkm_result
[2023-03-16 17:43:56,346] [INFO] Task succeeded: CheckM
[2023-03-16 17:43:56,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:43:56,349] [INFO] ===== Completeness check finished =====
[2023-03-16 17:43:56,349] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:43:56,349] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7699/markers.fasta)
[2023-03-16 17:43:56,351] [INFO] Task started: Blastn
[2023-03-16 17:43:56,351] [INFO] Running command: blastn -query OceanDNA-b7699/markers.fasta -db /var/lib/cwl/stg1de66833-071f-4d1b-9b6b-d7b6c86c0e6e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7699/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:43:57,157] [INFO] Task succeeded: Blastn
[2023-03-16 17:43:57,158] [INFO] Selected 11 target genomes.
[2023-03-16 17:43:57,159] [INFO] Target genome list was writen to OceanDNA-b7699/target_genomes_gtdb.txt
[2023-03-16 17:43:57,420] [INFO] Task started: fastANI
[2023-03-16 17:43:57,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae88f45-5f48-472c-b0a9-59215262c3c6/OceanDNA-b7699.fa --refList OceanDNA-b7699/target_genomes_gtdb.txt --output OceanDNA-b7699/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:44:01,126] [INFO] Task succeeded: fastANI
[2023-03-16 17:44:01,134] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:44:01,134] [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
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	95.4247	388	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	87.27	241	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_902510655.1	s__MAG-121220-bin8 sp902510655	84.2611	262	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	83.9548	265	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	83.9485	350	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	79.3127	283	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	79.0577	238	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635895.1	s__MAG-121220-bin8 sp902635895	78.6884	196	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.57	96.57	0.70	0.70	2	-
GCA_016780345.1	s__MAG-121220-bin8 sp016780345	78.4408	201	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.67	99.67	0.79	0.79	2	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	77.981	170	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_004214185.1	s__MAG-121220-bin8 sp004214185	77.9594	237	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	-
--------------------------------------------------------------------------------
[2023-03-16 17:44:01,134] [INFO] GTDB search result was written to OceanDNA-b7699/result_gtdb.tsv
[2023-03-16 17:44:01,134] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:44:01,136] [INFO] DFAST_QC result json was written to OceanDNA-b7699/dqc_result.json
[2023-03-16 17:44:01,136] [INFO] DFAST_QC completed!
[2023-03-16 17:44:01,136] [INFO] Total running time: 0h1m12s