[2023-03-19 00:15:41,730] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7627dfe-d79e-435b-9fb3-92e55c8ee6d1/dqc_reference
[2023-03-19 00:15:43,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,441] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,441] [INFO] Running command: cat /var/lib/cwl/stg6974c123-7ea5-43a2-8167-5c687271715b/OceanDNA-b5318.fa | prodigal -d OceanDNA-b5318/cds.fna -a OceanDNA-b5318/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:02,541] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:02,541] [INFO] Task started: HMMsearch
[2023-03-19 00:16:02,541] [INFO] Running command: hmmsearch --tblout OceanDNA-b5318/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7627dfe-d79e-435b-9fb3-92e55c8ee6d1/dqc_reference/reference_markers.hmm OceanDNA-b5318/protein.faa > /dev/null
[2023-03-19 00:16:02,742] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:02,742] [INFO] Found 6/6 markers.
[2023-03-19 00:16:02,760] [INFO] Query marker FASTA was written to OceanDNA-b5318/markers.fasta
[2023-03-19 00:16:02,761] [INFO] Task started: Blastn
[2023-03-19 00:16:02,761] [INFO] Running command: blastn -query OceanDNA-b5318/markers.fasta -db /var/lib/cwl/stgb7627dfe-d79e-435b-9fb3-92e55c8ee6d1/dqc_reference/reference_markers.fasta -out OceanDNA-b5318/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:03,295] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:03,295] [INFO] Selected 23 target genomes.
[2023-03-19 00:16:03,296] [INFO] Target genome list was writen to OceanDNA-b5318/target_genomes.txt
[2023-03-19 00:16:03,356] [INFO] Task started: fastANI
[2023-03-19 00:16:03,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg6974c123-7ea5-43a2-8167-5c687271715b/OceanDNA-b5318.fa --refList OceanDNA-b5318/target_genomes.txt --output OceanDNA-b5318/fastani_result.tsv --threads 1
[2023-03-19 00:16:17,608] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:17,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7627dfe-d79e-435b-9fb3-92e55c8ee6d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:17,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7627dfe-d79e-435b-9fb3-92e55c8ee6d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:17,613] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:17,613] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:17,613] [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	75.9283	59	927	95	below_threshold
Brumimicrobium aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	75.7687	51	927	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:17,614] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5318/tc_result.tsv
[2023-03-19 00:16:17,614] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:17,614] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:17,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7627dfe-d79e-435b-9fb3-92e55c8ee6d1/dqc_reference/checkm_data
[2023-03-19 00:16:17,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:17,676] [INFO] Task started: CheckM
[2023-03-19 00:16:17,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5318/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5318/checkm_input OceanDNA-b5318/checkm_result
[2023-03-19 00:17:07,608] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:07,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:07,611] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:07,611] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:07,611] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5318/markers.fasta)
[2023-03-19 00:17:07,612] [INFO] Task started: Blastn
[2023-03-19 00:17:07,612] [INFO] Running command: blastn -query OceanDNA-b5318/markers.fasta -db /var/lib/cwl/stgb7627dfe-d79e-435b-9fb3-92e55c8ee6d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5318/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:08,362] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:08,363] [INFO] Selected 23 target genomes.
[2023-03-19 00:17:08,363] [INFO] Target genome list was writen to OceanDNA-b5318/target_genomes_gtdb.txt
[2023-03-19 00:17:08,380] [INFO] Task started: fastANI
[2023-03-19 00:17:08,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg6974c123-7ea5-43a2-8167-5c687271715b/OceanDNA-b5318.fa --refList OceanDNA-b5318/target_genomes_gtdb.txt --output OceanDNA-b5318/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:20,523] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:20,531] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:17:20,531] [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_002734065.2	s__UBA4466 sp002734065	79.2066	479	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480145.1	s__UBA4466 sp905480145	77.6497	157	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480355.1	s__UBA4466 sp002389415	77.3556	136	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.55	99.55	0.81	0.81	2	-
GCA_013215515.1	s__UBA4466 sp013215515	77.1377	51	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402525.1	s__UBA4466 sp018402525	76.9894	93	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471375.1	s__UBA4466 sp002471375	76.8125	56	927	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	76.6067	70	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	96.56	96.56	0.90	0.90	2	-
GCA_905182335.1	s__UBA4466 sp905182335	76.5682	94	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.88	99.88	0.98	0.98	2	-
GCA_017984635.1	s__M0103 sp017984635	76.4851	71	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885545.1	s__M0103 sp009885545	76.439	60	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178305.1	s__CAIUKX01 sp016178305	76.3893	70	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709305.1	s__UBA4466 sp002709305	76.0274	75	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:20,532] [INFO] GTDB search result was written to OceanDNA-b5318/result_gtdb.tsv
[2023-03-19 00:17:20,532] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:20,533] [INFO] DFAST_QC result json was written to OceanDNA-b5318/dqc_result.json
[2023-03-19 00:17:20,533] [INFO] DFAST_QC completed!
[2023-03-19 00:17:20,533] [INFO] Total running time: 0h1m39s