[2023-03-14 11:33:34,963] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,963] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,963] [INFO] DQC Reference Directory: /var/lib/cwl/stgfefc80f8-7961-48eb-a771-8e5e3081d344/dqc_reference
[2023-03-14 11:33:36,181] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,182] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,182] [INFO] Running command: cat /var/lib/cwl/stg9d6a43b0-4387-4271-9da0-1c97d919f166/OceanDNA-b6749.fa | prodigal -d OceanDNA-b6749/cds.fna -a OceanDNA-b6749/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:56,597] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:56,598] [INFO] Task started: HMMsearch
[2023-03-14 11:33:56,598] [INFO] Running command: hmmsearch --tblout OceanDNA-b6749/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfefc80f8-7961-48eb-a771-8e5e3081d344/dqc_reference/reference_markers.hmm OceanDNA-b6749/protein.faa > /dev/null
[2023-03-14 11:33:56,820] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:56,821] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9d6a43b0-4387-4271-9da0-1c97d919f166/OceanDNA-b6749.fa]
[2023-03-14 11:33:56,840] [INFO] Query marker FASTA was written to OceanDNA-b6749/markers.fasta
[2023-03-14 11:33:56,840] [INFO] Task started: Blastn
[2023-03-14 11:33:56,840] [INFO] Running command: blastn -query OceanDNA-b6749/markers.fasta -db /var/lib/cwl/stgfefc80f8-7961-48eb-a771-8e5e3081d344/dqc_reference/reference_markers.fasta -out OceanDNA-b6749/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:57,373] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:57,374] [INFO] Selected 18 target genomes.
[2023-03-14 11:33:57,374] [INFO] Target genome list was writen to OceanDNA-b6749/target_genomes.txt
[2023-03-14 11:33:57,383] [INFO] Task started: fastANI
[2023-03-14 11:33:57,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d6a43b0-4387-4271-9da0-1c97d919f166/OceanDNA-b6749.fa --refList OceanDNA-b6749/target_genomes.txt --output OceanDNA-b6749/fastani_result.tsv --threads 1
[2023-03-14 11:34:11,236] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:11,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfefc80f8-7961-48eb-a771-8e5e3081d344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:11,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfefc80f8-7961-48eb-a771-8e5e3081d344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:11,245] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:11,245] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:34:11,246] [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
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	76.7964	167	945	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	76.7837	166	945	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_001653755.1	326320	326320	type	True	76.7503	104	945	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_000769435.1	326320	326320	type	True	76.7283	105	945	95	below_threshold
Dokdonia sinensis	strain=SH27	GCA_003688895.1	2479847	2479847	type	True	76.5049	146	945	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	76.0541	59	945	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.0246	60	945	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.0246	60	945	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	75.9997	65	945	95	below_threshold
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	75.9704	60	945	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	75.8544	61	945	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	75.7872	52	945	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	75.6536	60	945	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:11,246] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6749/tc_result.tsv
[2023-03-14 11:34:11,246] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:11,246] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:11,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfefc80f8-7961-48eb-a771-8e5e3081d344/dqc_reference/checkm_data
[2023-03-14 11:34:11,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:11,301] [INFO] Task started: CheckM
[2023-03-14 11:34:11,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6749/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6749/checkm_input OceanDNA-b6749/checkm_result
[2023-03-14 11:35:05,171] [INFO] Task succeeded: CheckM
[2023-03-14 11:35:05,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:35:05,174] [INFO] ===== Completeness check finished =====
[2023-03-14 11:35:05,174] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:35:05,174] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6749/markers.fasta)
[2023-03-14 11:35:05,174] [INFO] Task started: Blastn
[2023-03-14 11:35:05,174] [INFO] Running command: blastn -query OceanDNA-b6749/markers.fasta -db /var/lib/cwl/stgfefc80f8-7961-48eb-a771-8e5e3081d344/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6749/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:35:05,891] [INFO] Task succeeded: Blastn
[2023-03-14 11:35:05,892] [INFO] Selected 18 target genomes.
[2023-03-14 11:35:05,892] [INFO] Target genome list was writen to OceanDNA-b6749/target_genomes_gtdb.txt
[2023-03-14 11:35:05,928] [INFO] Task started: fastANI
[2023-03-14 11:35:05,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d6a43b0-4387-4271-9da0-1c97d919f166/OceanDNA-b6749.fa --refList OceanDNA-b6749/target_genomes_gtdb.txt --output OceanDNA-b6749/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:17,773] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:17,780] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:35:17,780] [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_002712765.1	s__Dokdonia sp002712765	99.5901	738	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	99.61	99.61	0.82	0.82	2	conclusive
GCF_900188275.1	s__Dokdonia pacifica	76.7964	167	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003095655.1	s__Dokdonia sp003095655	76.7752	89	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653755.1	s__Dokdonia donghaensis	76.7503	104	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	97.85	95.71	0.96	0.91	3	-
GCF_000355805.1	s__Dokdonia sp000355805	76.6737	102	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688895.1	s__Dokdonia sinensis	76.5188	145	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632745.1	s__Aquimarina aggregata	76.0541	59	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.64	98.63	0.93	0.92	3	-
GCF_002846555.1	s__Aquimarina sp002846555	75.9964	54	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520995.1	s__Aquimarina macrocephali	75.9704	60	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299525.1	s__Aquimarina sp900299525	75.9243	59	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	75.9186	64	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:35:17,781] [INFO] GTDB search result was written to OceanDNA-b6749/result_gtdb.tsv
[2023-03-14 11:35:17,781] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:17,782] [INFO] DFAST_QC result json was written to OceanDNA-b6749/dqc_result.json
[2023-03-14 11:35:17,782] [INFO] DFAST_QC completed!
[2023-03-14 11:35:17,782] [INFO] Total running time: 0h1m43s