[2023-03-15 03:02:04,958] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:02:04,958] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:02:04,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg17a31213-3927-42d9-a557-fcc891faf141/dqc_reference
[2023-03-15 03:02:06,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:02:06,580] [INFO] Task started: Prodigal
[2023-03-15 03:02:06,581] [INFO] Running command: cat /var/lib/cwl/stg7ad91b7d-09bc-476a-b1a1-89a12489c7a8/OceanDNA-b6164.fa | prodigal -d OceanDNA-b6164/cds.fna -a OceanDNA-b6164/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:02:26,420] [INFO] Task succeeded: Prodigal
[2023-03-15 03:02:26,421] [INFO] Task started: HMMsearch
[2023-03-15 03:02:26,421] [INFO] Running command: hmmsearch --tblout OceanDNA-b6164/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17a31213-3927-42d9-a557-fcc891faf141/dqc_reference/reference_markers.hmm OceanDNA-b6164/protein.faa > /dev/null
[2023-03-15 03:02:26,641] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:02:26,641] [INFO] Found 6/6 markers.
[2023-03-15 03:02:26,665] [INFO] Query marker FASTA was written to OceanDNA-b6164/markers.fasta
[2023-03-15 03:02:26,666] [INFO] Task started: Blastn
[2023-03-15 03:02:26,666] [INFO] Running command: blastn -query OceanDNA-b6164/markers.fasta -db /var/lib/cwl/stg17a31213-3927-42d9-a557-fcc891faf141/dqc_reference/reference_markers.fasta -out OceanDNA-b6164/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:02:27,207] [INFO] Task succeeded: Blastn
[2023-03-15 03:02:27,208] [INFO] Selected 33 target genomes.
[2023-03-15 03:02:27,208] [INFO] Target genome list was writen to OceanDNA-b6164/target_genomes.txt
[2023-03-15 03:02:27,226] [INFO] Task started: fastANI
[2023-03-15 03:02:27,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad91b7d-09bc-476a-b1a1-89a12489c7a8/OceanDNA-b6164.fa --refList OceanDNA-b6164/target_genomes.txt --output OceanDNA-b6164/fastani_result.tsv --threads 1
[2023-03-15 03:02:45,012] [INFO] Task succeeded: fastANI
[2023-03-15 03:02:45,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17a31213-3927-42d9-a557-fcc891faf141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:02:45,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17a31213-3927-42d9-a557-fcc891faf141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:02:45,016] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:02:45,016] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:02:45,016] [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
Croceimicrobium hydrocarbonivorans	strain=A20-9	GCA_014524565.1	2761580	2761580	type	True	78.2373	288	903	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:02:45,017] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6164/tc_result.tsv
[2023-03-15 03:02:45,017] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:02:45,017] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:02:45,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17a31213-3927-42d9-a557-fcc891faf141/dqc_reference/checkm_data
[2023-03-15 03:02:45,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:02:45,028] [INFO] Task started: CheckM
[2023-03-15 03:02:45,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6164/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6164/checkm_input OceanDNA-b6164/checkm_result
[2023-03-15 03:03:35,799] [INFO] Task succeeded: CheckM
[2023-03-15 03:03:35,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:03:35,805] [INFO] ===== Completeness check finished =====
[2023-03-15 03:03:35,805] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:03:35,805] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6164/markers.fasta)
[2023-03-15 03:03:35,806] [INFO] Task started: Blastn
[2023-03-15 03:03:35,806] [INFO] Running command: blastn -query OceanDNA-b6164/markers.fasta -db /var/lib/cwl/stg17a31213-3927-42d9-a557-fcc891faf141/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6164/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:03:36,561] [INFO] Task succeeded: Blastn
[2023-03-15 03:03:36,564] [INFO] Selected 37 target genomes.
[2023-03-15 03:03:36,564] [INFO] Target genome list was writen to OceanDNA-b6164/target_genomes_gtdb.txt
[2023-03-15 03:03:36,591] [INFO] Task started: fastANI
[2023-03-15 03:03:36,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad91b7d-09bc-476a-b1a1-89a12489c7a8/OceanDNA-b6164.fa --refList OceanDNA-b6164/target_genomes_gtdb.txt --output OceanDNA-b6164/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:03:57,180] [INFO] Task succeeded: fastANI
[2023-03-15 03:03:57,184] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:03:57,184] [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_002501205.1	s__Croceimicrobium sp002501205	78.2574	260	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	99.91	99.91	0.95	0.95	2	-
GCF_014524565.1	s__Croceimicrobium hydrocarbonivorans	78.2504	287	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795025.1	s__Croceimicrobium sp017795025	77.8832	236	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401735.1	s__Croceimicrobium sp018401735	76.5576	116	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045865.1	s__Croceimicrobium sp003045865	76.5144	113	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:03:57,186] [INFO] GTDB search result was written to OceanDNA-b6164/result_gtdb.tsv
[2023-03-15 03:03:57,188] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:03:57,189] [INFO] DFAST_QC result json was written to OceanDNA-b6164/dqc_result.json
[2023-03-15 03:03:57,189] [INFO] DFAST_QC completed!
[2023-03-15 03:03:57,189] [INFO] Total running time: 0h1m52s