[2023-03-19 04:11:06,926] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg4811bbec-7a15-407d-a781-befd8b4c96b8/dqc_reference
[2023-03-19 04:11:08,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,645] [INFO] Running command: cat /var/lib/cwl/stgd2c3f1cf-1896-406a-8f07-c7d794eb3e51/OceanDNA-b5321.fa | prodigal -d OceanDNA-b5321/cds.fna -a OceanDNA-b5321/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:24,687] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:24,688] [INFO] Task started: HMMsearch
[2023-03-19 04:11:24,688] [INFO] Running command: hmmsearch --tblout OceanDNA-b5321/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4811bbec-7a15-407d-a781-befd8b4c96b8/dqc_reference/reference_markers.hmm OceanDNA-b5321/protein.faa > /dev/null
[2023-03-19 04:11:24,890] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:24,891] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd2c3f1cf-1896-406a-8f07-c7d794eb3e51/OceanDNA-b5321.fa]
[2023-03-19 04:11:24,912] [INFO] Query marker FASTA was written to OceanDNA-b5321/markers.fasta
[2023-03-19 04:11:24,912] [INFO] Task started: Blastn
[2023-03-19 04:11:24,912] [INFO] Running command: blastn -query OceanDNA-b5321/markers.fasta -db /var/lib/cwl/stg4811bbec-7a15-407d-a781-befd8b4c96b8/dqc_reference/reference_markers.fasta -out OceanDNA-b5321/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:25,492] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:25,493] [INFO] Selected 22 target genomes.
[2023-03-19 04:11:25,493] [INFO] Target genome list was writen to OceanDNA-b5321/target_genomes.txt
[2023-03-19 04:11:25,506] [INFO] Task started: fastANI
[2023-03-19 04:11:25,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c3f1cf-1896-406a-8f07-c7d794eb3e51/OceanDNA-b5321.fa --refList OceanDNA-b5321/target_genomes.txt --output OceanDNA-b5321/fastani_result.tsv --threads 1
[2023-03-19 04:11:39,454] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:39,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4811bbec-7a15-407d-a781-befd8b4c96b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:39,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4811bbec-7a15-407d-a781-befd8b4c96b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:39,459] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:39,459] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:39,459] [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
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.5394	68	736	95	below_threshold
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	76.0741	61	736	95	below_threshold
Brumimicrobium aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	76.0555	55	736	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:39,459] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5321/tc_result.tsv
[2023-03-19 04:11:39,459] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:39,459] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:39,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4811bbec-7a15-407d-a781-befd8b4c96b8/dqc_reference/checkm_data
[2023-03-19 04:11:39,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:39,464] [INFO] Task started: CheckM
[2023-03-19 04:11:39,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5321/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5321/checkm_input OceanDNA-b5321/checkm_result
[2023-03-19 04:12:22,790] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:22,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:22,793] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:22,793] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:22,794] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5321/markers.fasta)
[2023-03-19 04:12:22,794] [INFO] Task started: Blastn
[2023-03-19 04:12:22,794] [INFO] Running command: blastn -query OceanDNA-b5321/markers.fasta -db /var/lib/cwl/stg4811bbec-7a15-407d-a781-befd8b4c96b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5321/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:23,710] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:23,710] [INFO] Selected 21 target genomes.
[2023-03-19 04:12:23,711] [INFO] Target genome list was writen to OceanDNA-b5321/target_genomes_gtdb.txt
[2023-03-19 04:12:23,833] [INFO] Task started: fastANI
[2023-03-19 04:12:23,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c3f1cf-1896-406a-8f07-c7d794eb3e51/OceanDNA-b5321.fa --refList OceanDNA-b5321/target_genomes_gtdb.txt --output OceanDNA-b5321/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:35,158] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:35,168] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:12:35,168] [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_018402525.1	s__UBA4466 sp018402525	77.7728	198	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733985.1	s__UBA4466 sp002733985	77.1714	82	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	96.56	96.56	0.90	0.90	2	-
GCA_905480145.1	s__UBA4466 sp905480145	77.057	100	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182335.1	s__UBA4466 sp905182335	77.0567	101	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.88	99.88	0.98	0.98	2	-
GCA_013215515.1	s__UBA4466 sp013215515	76.9244	62	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002734065.2	s__UBA4466 sp002734065	76.7986	102	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478665.1	s__UBA4466 sp905478665	76.7509	85	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003149635.1	s__UBA4466 sp003149635	76.5933	52	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885545.1	s__M0103 sp009885545	76.5504	69	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194605.1	s__Fluviicola taffensis	76.5394	68	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480355.1	s__UBA4466 sp002389415	76.3856	78	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.55	99.55	0.81	0.81	2	-
GCA_016178305.1	s__CAIUKX01 sp016178305	76.3096	78	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471375.1	s__UBA4466 sp002471375	76.2254	59	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930085.1	s__M0103 sp903930085	76.1894	50	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402975.1	s__Brumimicrobium aurantiacum	76.108	53	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025005.1	s__Brumimicrobium mesophilum	76.0857	59	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:35,168] [INFO] GTDB search result was written to OceanDNA-b5321/result_gtdb.tsv
[2023-03-19 04:12:35,168] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:35,170] [INFO] DFAST_QC result json was written to OceanDNA-b5321/dqc_result.json
[2023-03-19 04:12:35,170] [INFO] DFAST_QC completed!
[2023-03-19 04:12:35,170] [INFO] Total running time: 0h1m28s