[2023-03-18 02:42:32,930] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:42:32,930] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:42:32,930] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1326a04-ac7a-495f-bf98-62f5afb859b1/dqc_reference
[2023-03-18 02:42:34,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:42:34,116] [INFO] Task started: Prodigal
[2023-03-18 02:42:34,117] [INFO] Running command: cat /var/lib/cwl/stga8a84db8-8a62-494d-8d6e-019ab48edf12/OceanDNA-b11077.fa | prodigal -d OceanDNA-b11077/cds.fna -a OceanDNA-b11077/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:42:43,979] [INFO] Task succeeded: Prodigal
[2023-03-18 02:42:43,980] [INFO] Task started: HMMsearch
[2023-03-18 02:42:43,980] [INFO] Running command: hmmsearch --tblout OceanDNA-b11077/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1326a04-ac7a-495f-bf98-62f5afb859b1/dqc_reference/reference_markers.hmm OceanDNA-b11077/protein.faa > /dev/null
[2023-03-18 02:42:44,147] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:42:44,148] [INFO] Found 6/6 markers.
[2023-03-18 02:42:44,158] [INFO] Query marker FASTA was written to OceanDNA-b11077/markers.fasta
[2023-03-18 02:42:44,159] [INFO] Task started: Blastn
[2023-03-18 02:42:44,159] [INFO] Running command: blastn -query OceanDNA-b11077/markers.fasta -db /var/lib/cwl/stgf1326a04-ac7a-495f-bf98-62f5afb859b1/dqc_reference/reference_markers.fasta -out OceanDNA-b11077/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:42:44,698] [INFO] Task succeeded: Blastn
[2023-03-18 02:42:44,699] [INFO] Selected 29 target genomes.
[2023-03-18 02:42:44,699] [INFO] Target genome list was writen to OceanDNA-b11077/target_genomes.txt
[2023-03-18 02:42:44,712] [INFO] Task started: fastANI
[2023-03-18 02:42:44,712] [INFO] Running command: fastANI --query /var/lib/cwl/stga8a84db8-8a62-494d-8d6e-019ab48edf12/OceanDNA-b11077.fa --refList OceanDNA-b11077/target_genomes.txt --output OceanDNA-b11077/fastani_result.tsv --threads 1
[2023-03-18 02:43:00,228] [INFO] Task succeeded: fastANI
[2023-03-18 02:43:00,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1326a04-ac7a-495f-bf98-62f5afb859b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:43:00,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1326a04-ac7a-495f-bf98-62f5afb859b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:43:00,229] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:43:00,229] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:43:00,229] [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
--------------------------------------------------------------------------------
[2023-03-18 02:43:00,229] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11077/tc_result.tsv
[2023-03-18 02:43:00,230] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:43:00,230] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:43:00,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1326a04-ac7a-495f-bf98-62f5afb859b1/dqc_reference/checkm_data
[2023-03-18 02:43:00,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:43:00,235] [INFO] Task started: CheckM
[2023-03-18 02:43:00,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11077/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11077/checkm_input OceanDNA-b11077/checkm_result
[2023-03-18 02:43:29,425] [INFO] Task succeeded: CheckM
[2023-03-18 02:43:29,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.86%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:43:29,427] [INFO] ===== Completeness check finished =====
[2023-03-18 02:43:29,427] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:43:29,428] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11077/markers.fasta)
[2023-03-18 02:43:29,428] [INFO] Task started: Blastn
[2023-03-18 02:43:29,428] [INFO] Running command: blastn -query OceanDNA-b11077/markers.fasta -db /var/lib/cwl/stgf1326a04-ac7a-495f-bf98-62f5afb859b1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11077/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:43:30,177] [INFO] Task succeeded: Blastn
[2023-03-18 02:43:30,178] [INFO] Selected 9 target genomes.
[2023-03-18 02:43:30,178] [INFO] Target genome list was writen to OceanDNA-b11077/target_genomes_gtdb.txt
[2023-03-18 02:43:30,343] [INFO] Task started: fastANI
[2023-03-18 02:43:30,343] [INFO] Running command: fastANI --query /var/lib/cwl/stga8a84db8-8a62-494d-8d6e-019ab48edf12/OceanDNA-b11077.fa --refList OceanDNA-b11077/target_genomes_gtdb.txt --output OceanDNA-b11077/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:43:32,823] [INFO] Task succeeded: fastANI
[2023-03-18 02:43:32,829] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:43:32,829] [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_009937085.1	s__UBA7446 sp009937085	97.4344	336	414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003331305.1	s__UBA7446 sp002470745	85.6145	304	414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.36	99.14	0.86	0.83	3	-
GCA_017856205.1	s__UBA7446 sp017856205	80.5026	270	414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478685.1	s__UBA7446 sp002478685	79.98	255	414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.74	99.74	0.91	0.91	3	-
GCA_009886265.1	s__UBA7446 sp009886265	78.4692	151	414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862705.1	s__UBA7446 sp002862705	77.8457	157	414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.06	98.27	0.87	0.83	14	-
GCA_002862645.1	s__UBA7446 sp002862645	77.6622	119	414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	95.15	95.15	0.79	0.79	2	-
GCA_002313325.1	s__UBA7446 sp002313325	77.5816	92	414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.90	99.90	0.92	0.92	2	-
GCA_002698745.1	s__UBA7446 sp002698745	77.2775	85	414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:43:32,830] [INFO] GTDB search result was written to OceanDNA-b11077/result_gtdb.tsv
[2023-03-18 02:43:32,830] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:43:32,831] [INFO] DFAST_QC result json was written to OceanDNA-b11077/dqc_result.json
[2023-03-18 02:43:32,831] [INFO] DFAST_QC completed!
[2023-03-18 02:43:32,831] [INFO] Total running time: 0h0m60s