[2023-03-14 10:55:58,906] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,906] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,906] [INFO] DQC Reference Directory: /var/lib/cwl/stga896779e-0f20-46a1-9583-a48b983be5e9/dqc_reference
[2023-03-14 10:56:00,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,677] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,677] [INFO] Running command: cat /var/lib/cwl/stg8ce25c83-36b8-4832-ae78-018585957dc2/OceanDNA-b12620.fa | prodigal -d OceanDNA-b12620/cds.fna -a OceanDNA-b12620/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:20,115] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:20,115] [INFO] Task started: HMMsearch
[2023-03-14 10:56:20,115] [INFO] Running command: hmmsearch --tblout OceanDNA-b12620/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga896779e-0f20-46a1-9583-a48b983be5e9/dqc_reference/reference_markers.hmm OceanDNA-b12620/protein.faa > /dev/null
[2023-03-14 10:56:20,374] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:20,374] [INFO] Found 6/6 markers.
[2023-03-14 10:56:20,406] [INFO] Query marker FASTA was written to OceanDNA-b12620/markers.fasta
[2023-03-14 10:56:20,406] [INFO] Task started: Blastn
[2023-03-14 10:56:20,406] [INFO] Running command: blastn -query OceanDNA-b12620/markers.fasta -db /var/lib/cwl/stga896779e-0f20-46a1-9583-a48b983be5e9/dqc_reference/reference_markers.fasta -out OceanDNA-b12620/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:20,963] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:20,964] [INFO] Selected 32 target genomes.
[2023-03-14 10:56:20,964] [INFO] Target genome list was writen to OceanDNA-b12620/target_genomes.txt
[2023-03-14 10:56:20,981] [INFO] Task started: fastANI
[2023-03-14 10:56:20,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce25c83-36b8-4832-ae78-018585957dc2/OceanDNA-b12620.fa --refList OceanDNA-b12620/target_genomes.txt --output OceanDNA-b12620/fastani_result.tsv --threads 1
[2023-03-14 10:56:40,435] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:40,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga896779e-0f20-46a1-9583-a48b983be5e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:40,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga896779e-0f20-46a1-9583-a48b983be5e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:40,440] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:40,440] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:40,440] [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
Vicingus serpentipes	strain=NCIMB 15042	GCA_007993035.1	1926625	1926625	type	True	76.7582	185	1013	95	below_threshold
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	75.6602	56	1013	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	75.5926	53	1013	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	75.5926	53	1013	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:40,451] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12620/tc_result.tsv
[2023-03-14 10:56:40,451] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:40,451] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:40,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga896779e-0f20-46a1-9583-a48b983be5e9/dqc_reference/checkm_data
[2023-03-14 10:56:40,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:40,456] [INFO] Task started: CheckM
[2023-03-14 10:56:40,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12620/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12620/checkm_input OceanDNA-b12620/checkm_result
[2023-03-14 10:57:29,395] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:29,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:29,398] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:29,398] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:29,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12620/markers.fasta)
[2023-03-14 10:57:29,399] [INFO] Task started: Blastn
[2023-03-14 10:57:29,399] [INFO] Running command: blastn -query OceanDNA-b12620/markers.fasta -db /var/lib/cwl/stga896779e-0f20-46a1-9583-a48b983be5e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12620/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:30,148] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:30,149] [INFO] Selected 11 target genomes.
[2023-03-14 10:57:30,149] [INFO] Target genome list was writen to OceanDNA-b12620/target_genomes_gtdb.txt
[2023-03-14 10:57:30,186] [INFO] Task started: fastANI
[2023-03-14 10:57:30,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce25c83-36b8-4832-ae78-018585957dc2/OceanDNA-b12620.fa --refList OceanDNA-b12620/target_genomes_gtdb.txt --output OceanDNA-b12620/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:37,018] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:37,024] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:37,025] [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_000961845.1	s__BRH-c54 sp000961845	99.6711	885	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002359215.1	s__BRH-c54 sp002359215	93.3651	866	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	99.41	98.22	0.97	0.91	4	-
GCA_002841035.1	s__BRH-c54 sp002841035	80.3418	302	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002770955.1	s__BRH-c54 sp002770955	80.0624	408	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	99.41	99.41	0.88	0.88	2	-
GCA_015075325.1	s__Vicingus sp015075325	77.1533	189	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	96.71	96.71	0.84	0.84	2	-
GCA_016183805.1	s__Vicingus sp016183805	76.801	199	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002790175.1	s__GCA-002793235 sp002790175	76.8006	151	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	99.29	99.29	0.84	0.84	2	-
GCA_905479915.1	s__GCA-002793235 sp905479915	76.7771	155	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993035.1	s__Vicingus serpentipes	76.7451	186	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479995.1	s__GCA-002793235 sp905479995	76.6052	149	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:37,025] [INFO] GTDB search result was written to OceanDNA-b12620/result_gtdb.tsv
[2023-03-14 10:57:37,025] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:37,026] [INFO] DFAST_QC result json was written to OceanDNA-b12620/dqc_result.json
[2023-03-14 10:57:37,026] [INFO] DFAST_QC completed!
[2023-03-14 10:57:37,026] [INFO] Total running time: 0h1m38s