[2023-03-19 02:51:48,242] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:51:48,242] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:51:48,242] [INFO] DQC Reference Directory: /var/lib/cwl/stg4924311d-712d-4d72-a8dd-164a6c5cae07/dqc_reference
[2023-03-19 02:51:49,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:51:49,378] [INFO] Task started: Prodigal
[2023-03-19 02:51:49,378] [INFO] Running command: cat /var/lib/cwl/stgd36fa66c-54d9-4728-bc47-92aab1c950f6/OceanDNA-b10950.fa | prodigal -d OceanDNA-b10950/cds.fna -a OceanDNA-b10950/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:52:01,069] [INFO] Task succeeded: Prodigal
[2023-03-19 02:52:01,069] [INFO] Task started: HMMsearch
[2023-03-19 02:52:01,069] [INFO] Running command: hmmsearch --tblout OceanDNA-b10950/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4924311d-712d-4d72-a8dd-164a6c5cae07/dqc_reference/reference_markers.hmm OceanDNA-b10950/protein.faa > /dev/null
[2023-03-19 02:52:01,251] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:52:01,251] [INFO] Found 6/6 markers.
[2023-03-19 02:52:01,264] [INFO] Query marker FASTA was written to OceanDNA-b10950/markers.fasta
[2023-03-19 02:52:01,265] [INFO] Task started: Blastn
[2023-03-19 02:52:01,265] [INFO] Running command: blastn -query OceanDNA-b10950/markers.fasta -db /var/lib/cwl/stg4924311d-712d-4d72-a8dd-164a6c5cae07/dqc_reference/reference_markers.fasta -out OceanDNA-b10950/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:52:01,797] [INFO] Task succeeded: Blastn
[2023-03-19 02:52:01,817] [INFO] Selected 36 target genomes.
[2023-03-19 02:52:01,818] [INFO] Target genome list was writen to OceanDNA-b10950/target_genomes.txt
[2023-03-19 02:52:01,831] [INFO] Task started: fastANI
[2023-03-19 02:52:01,831] [INFO] Running command: fastANI --query /var/lib/cwl/stgd36fa66c-54d9-4728-bc47-92aab1c950f6/OceanDNA-b10950.fa --refList OceanDNA-b10950/target_genomes.txt --output OceanDNA-b10950/fastani_result.tsv --threads 1
[2023-03-19 02:52:18,849] [INFO] Task succeeded: fastANI
[2023-03-19 02:52:18,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4924311d-712d-4d72-a8dd-164a6c5cae07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:52:18,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4924311d-712d-4d72-a8dd-164a6c5cae07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:52:18,849] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:52:18,850] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:52:18,850] [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
--------------------------------------------------------------------------------
[2023-03-19 02:52:18,855] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10950/tc_result.tsv
[2023-03-19 02:52:18,855] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:52:18,855] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:52:18,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4924311d-712d-4d72-a8dd-164a6c5cae07/dqc_reference/checkm_data
[2023-03-19 02:52:18,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:52:18,869] [INFO] Task started: CheckM
[2023-03-19 02:52:18,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10950/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10950/checkm_input OceanDNA-b10950/checkm_result
[2023-03-19 02:52:52,777] [INFO] Task succeeded: CheckM
[2023-03-19 02:52:52,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:52:52,797] [INFO] ===== Completeness check finished =====
[2023-03-19 02:52:52,797] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:52:52,797] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10950/markers.fasta)
[2023-03-19 02:52:52,797] [INFO] Task started: Blastn
[2023-03-19 02:52:52,797] [INFO] Running command: blastn -query OceanDNA-b10950/markers.fasta -db /var/lib/cwl/stg4924311d-712d-4d72-a8dd-164a6c5cae07/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10950/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:52:53,581] [INFO] Task succeeded: Blastn
[2023-03-19 02:52:53,582] [INFO] Selected 27 target genomes.
[2023-03-19 02:52:53,582] [INFO] Target genome list was writen to OceanDNA-b10950/target_genomes_gtdb.txt
[2023-03-19 02:52:53,607] [INFO] Task started: fastANI
[2023-03-19 02:52:53,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgd36fa66c-54d9-4728-bc47-92aab1c950f6/OceanDNA-b10950.fa --refList OceanDNA-b10950/target_genomes_gtdb.txt --output OceanDNA-b10950/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:53:04,814] [INFO] Task succeeded: fastANI
[2023-03-19 02:53:04,819] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:53:04,819] [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_905478905.1	s__UBA7428 sp905478905	82.2812	350	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
GCA_002477625.1	s__UBA7428 sp002477625	77.2043	55	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
GCA_011526285.1	s__UBA7428 sp011526285	77.0792	110	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608425.1	s__UBA7428 sp018608425	76.868	52	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181615.1	s__UBA7428 sp905181615	76.6945	58	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_011526265.1	s__UBA7428 sp011526265	76.3877	77	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526335.1	s__UBA7428 sp011526335	76.1875	61	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:53:04,824] [INFO] GTDB search result was written to OceanDNA-b10950/result_gtdb.tsv
[2023-03-19 02:53:04,830] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:53:04,837] [INFO] DFAST_QC result json was written to OceanDNA-b10950/dqc_result.json
[2023-03-19 02:53:04,837] [INFO] DFAST_QC completed!
[2023-03-19 02:53:04,837] [INFO] Total running time: 0h1m17s