[2023-03-15 10:09:49,679] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:09:49,679] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:09:49,680] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd094e1e-48e8-45e4-a937-1e14f3be4ed8/dqc_reference
[2023-03-15 10:09:51,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:09:51,537] [INFO] Task started: Prodigal
[2023-03-15 10:09:51,537] [INFO] Running command: cat /var/lib/cwl/stgd4277183-1606-4d22-8c61-6f08eefd2ff1/OceanDNA-b5372.fa | prodigal -d OceanDNA-b5372/cds.fna -a OceanDNA-b5372/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:10:11,381] [INFO] Task succeeded: Prodigal
[2023-03-15 10:10:11,381] [INFO] Task started: HMMsearch
[2023-03-15 10:10:11,381] [INFO] Running command: hmmsearch --tblout OceanDNA-b5372/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd094e1e-48e8-45e4-a937-1e14f3be4ed8/dqc_reference/reference_markers.hmm OceanDNA-b5372/protein.faa > /dev/null
[2023-03-15 10:10:11,578] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:10:11,578] [INFO] Found 6/6 markers.
[2023-03-15 10:10:11,595] [INFO] Query marker FASTA was written to OceanDNA-b5372/markers.fasta
[2023-03-15 10:10:11,597] [INFO] Task started: Blastn
[2023-03-15 10:10:11,597] [INFO] Running command: blastn -query OceanDNA-b5372/markers.fasta -db /var/lib/cwl/stgfd094e1e-48e8-45e4-a937-1e14f3be4ed8/dqc_reference/reference_markers.fasta -out OceanDNA-b5372/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:12,142] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:12,142] [INFO] Selected 23 target genomes.
[2023-03-15 10:10:12,143] [INFO] Target genome list was writen to OceanDNA-b5372/target_genomes.txt
[2023-03-15 10:10:12,210] [INFO] Task started: fastANI
[2023-03-15 10:10:12,210] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4277183-1606-4d22-8c61-6f08eefd2ff1/OceanDNA-b5372.fa --refList OceanDNA-b5372/target_genomes.txt --output OceanDNA-b5372/fastani_result.tsv --threads 1
[2023-03-15 10:10:27,616] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:27,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd094e1e-48e8-45e4-a937-1e14f3be4ed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:10:27,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd094e1e-48e8-45e4-a937-1e14f3be4ed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:10:27,619] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:10:27,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:10:27,619] [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	75.8844	63	918	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:10:27,620] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5372/tc_result.tsv
[2023-03-15 10:10:27,620] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:10:27,620] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:10:27,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd094e1e-48e8-45e4-a937-1e14f3be4ed8/dqc_reference/checkm_data
[2023-03-15 10:10:27,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:10:27,680] [INFO] Task started: CheckM
[2023-03-15 10:10:27,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5372/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5372/checkm_input OceanDNA-b5372/checkm_result
[2023-03-15 10:11:19,988] [INFO] Task succeeded: CheckM
[2023-03-15 10:11:19,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:11:20,085] [INFO] ===== Completeness check finished =====
[2023-03-15 10:11:20,085] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:11:20,085] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5372/markers.fasta)
[2023-03-15 10:11:20,086] [INFO] Task started: Blastn
[2023-03-15 10:11:20,086] [INFO] Running command: blastn -query OceanDNA-b5372/markers.fasta -db /var/lib/cwl/stgfd094e1e-48e8-45e4-a937-1e14f3be4ed8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5372/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:11:20,857] [INFO] Task succeeded: Blastn
[2023-03-15 10:11:20,870] [INFO] Selected 19 target genomes.
[2023-03-15 10:11:20,870] [INFO] Target genome list was writen to OceanDNA-b5372/target_genomes_gtdb.txt
[2023-03-15 10:11:21,135] [INFO] Task started: fastANI
[2023-03-15 10:11:21,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4277183-1606-4d22-8c61-6f08eefd2ff1/OceanDNA-b5372.fa --refList OceanDNA-b5372/target_genomes_gtdb.txt --output OceanDNA-b5372/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:11:30,136] [INFO] Task succeeded: fastANI
[2023-03-15 10:11:30,144] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:11:30,144] [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_013215515.1	s__UBA4466 sp013215515	80.753	378	918	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	77.863	112	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.88	99.88	0.98	0.98	2	-
GCA_905480355.1	s__UBA4466 sp002389415	77.8307	96	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.55	99.55	0.81	0.81	2	-
GCA_002471375.1	s__UBA4466 sp002471375	77.4732	82	918	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	77.2274	89	918	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	77.0248	91	918	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	76.9933	111	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665275.1	s__UBA4466 sp015665275	76.8145	111	918	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	76.627	98	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427735.1	s__UBA4466 sp002427735	76.5184	100	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479845.1	s__UBA4466 sp905479845	76.5085	82	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945495.1	s__M0103 sp903945495	76.4498	91	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
--------------------------------------------------------------------------------
[2023-03-15 10:11:30,147] [INFO] GTDB search result was written to OceanDNA-b5372/result_gtdb.tsv
[2023-03-15 10:11:30,147] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:11:30,151] [INFO] DFAST_QC result json was written to OceanDNA-b5372/dqc_result.json
[2023-03-15 10:11:30,151] [INFO] DFAST_QC completed!
[2023-03-15 10:11:30,151] [INFO] Total running time: 0h1m40s