[2023-03-17 11:38:03,664] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:38:03,666] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:38:03,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg87dd1f78-acb9-4759-a92b-0efd200b1f43/dqc_reference
[2023-03-17 11:38:04,797] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:38:04,798] [INFO] Task started: Prodigal
[2023-03-17 11:38:04,798] [INFO] Running command: cat /var/lib/cwl/stgc3b157cc-f4cc-47ea-b7c9-93477f9b0865/OceanDNA-b5575.fa | prodigal -d OceanDNA-b5575/cds.fna -a OceanDNA-b5575/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:38:16,276] [INFO] Task succeeded: Prodigal
[2023-03-17 11:38:16,276] [INFO] Task started: HMMsearch
[2023-03-17 11:38:16,276] [INFO] Running command: hmmsearch --tblout OceanDNA-b5575/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87dd1f78-acb9-4759-a92b-0efd200b1f43/dqc_reference/reference_markers.hmm OceanDNA-b5575/protein.faa > /dev/null
[2023-03-17 11:38:16,442] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:38:16,442] [INFO] Found 6/6 markers.
[2023-03-17 11:38:16,468] [INFO] Query marker FASTA was written to OceanDNA-b5575/markers.fasta
[2023-03-17 11:38:16,468] [INFO] Task started: Blastn
[2023-03-17 11:38:16,468] [INFO] Running command: blastn -query OceanDNA-b5575/markers.fasta -db /var/lib/cwl/stg87dd1f78-acb9-4759-a92b-0efd200b1f43/dqc_reference/reference_markers.fasta -out OceanDNA-b5575/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:38:17,009] [INFO] Task succeeded: Blastn
[2023-03-17 11:38:17,016] [INFO] Selected 26 target genomes.
[2023-03-17 11:38:17,016] [INFO] Target genome list was writen to OceanDNA-b5575/target_genomes.txt
[2023-03-17 11:38:17,029] [INFO] Task started: fastANI
[2023-03-17 11:38:17,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3b157cc-f4cc-47ea-b7c9-93477f9b0865/OceanDNA-b5575.fa --refList OceanDNA-b5575/target_genomes.txt --output OceanDNA-b5575/fastani_result.tsv --threads 1
[2023-03-17 11:38:32,151] [INFO] Task succeeded: fastANI
[2023-03-17 11:38:32,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87dd1f78-acb9-4759-a92b-0efd200b1f43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:38:32,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87dd1f78-acb9-4759-a92b-0efd200b1f43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:38:32,152] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:38:32,152] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:38:32,152] [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
--------------------------------------------------------------------------------
[2023-03-17 11:38:32,154] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5575/tc_result.tsv
[2023-03-17 11:38:32,157] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:38:32,158] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:38:32,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87dd1f78-acb9-4759-a92b-0efd200b1f43/dqc_reference/checkm_data
[2023-03-17 11:38:32,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:38:32,189] [INFO] Task started: CheckM
[2023-03-17 11:38:32,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5575/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5575/checkm_input OceanDNA-b5575/checkm_result
[2023-03-17 11:39:05,437] [INFO] Task succeeded: CheckM
[2023-03-17 11:39:05,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:39:05,456] [INFO] ===== Completeness check finished =====
[2023-03-17 11:39:05,456] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:39:05,456] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5575/markers.fasta)
[2023-03-17 11:39:05,456] [INFO] Task started: Blastn
[2023-03-17 11:39:05,457] [INFO] Running command: blastn -query OceanDNA-b5575/markers.fasta -db /var/lib/cwl/stg87dd1f78-acb9-4759-a92b-0efd200b1f43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5575/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:39:06,229] [INFO] Task succeeded: Blastn
[2023-03-17 11:39:06,235] [INFO] Selected 24 target genomes.
[2023-03-17 11:39:06,235] [INFO] Target genome list was writen to OceanDNA-b5575/target_genomes_gtdb.txt
[2023-03-17 11:39:06,257] [INFO] Task started: fastANI
[2023-03-17 11:39:06,257] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3b157cc-f4cc-47ea-b7c9-93477f9b0865/OceanDNA-b5575.fa --refList OceanDNA-b5575/target_genomes_gtdb.txt --output OceanDNA-b5575/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:39:18,312] [INFO] Task succeeded: fastANI
[2023-03-17 11:39:18,316] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:39:18,316] [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_002293185.1	s__UBA952 sp002293185	81.4052	318	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295165.1	s__UBA952 sp004295165	80.5537	215	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872115.1	s__UBA952 sp016872115	78.8162	254	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478565.1	s__UBA952 sp002478565	77.6567	165	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.96	99.96	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:39:18,318] [INFO] GTDB search result was written to OceanDNA-b5575/result_gtdb.tsv
[2023-03-17 11:39:18,319] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:39:18,320] [INFO] DFAST_QC result json was written to OceanDNA-b5575/dqc_result.json
[2023-03-17 11:39:18,320] [INFO] DFAST_QC completed!
[2023-03-17 11:39:18,321] [INFO] Total running time: 0h1m15s