[2023-03-18 03:45:10,280] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,280] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ba23fa4-b44a-47d2-9ee8-4dc14154c262/dqc_reference
[2023-03-18 03:45:12,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,144] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,144] [INFO] Running command: cat /var/lib/cwl/stgd07ac0d7-e5dd-4d5b-a735-67f64380a755/OceanDNA-b3477.fa | prodigal -d OceanDNA-b3477/cds.fna -a OceanDNA-b3477/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:33,262] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:33,262] [INFO] Task started: HMMsearch
[2023-03-18 03:45:33,263] [INFO] Running command: hmmsearch --tblout OceanDNA-b3477/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ba23fa4-b44a-47d2-9ee8-4dc14154c262/dqc_reference/reference_markers.hmm OceanDNA-b3477/protein.faa > /dev/null
[2023-03-18 03:45:33,504] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:33,505] [INFO] Found 6/6 markers.
[2023-03-18 03:45:33,526] [INFO] Query marker FASTA was written to OceanDNA-b3477/markers.fasta
[2023-03-18 03:45:33,527] [INFO] Task started: Blastn
[2023-03-18 03:45:33,527] [INFO] Running command: blastn -query OceanDNA-b3477/markers.fasta -db /var/lib/cwl/stg6ba23fa4-b44a-47d2-9ee8-4dc14154c262/dqc_reference/reference_markers.fasta -out OceanDNA-b3477/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:34,061] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:34,062] [INFO] Selected 32 target genomes.
[2023-03-18 03:45:34,062] [INFO] Target genome list was writen to OceanDNA-b3477/target_genomes.txt
[2023-03-18 03:45:34,079] [INFO] Task started: fastANI
[2023-03-18 03:45:34,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07ac0d7-e5dd-4d5b-a735-67f64380a755/OceanDNA-b3477.fa --refList OceanDNA-b3477/target_genomes.txt --output OceanDNA-b3477/fastani_result.tsv --threads 1
[2023-03-18 03:45:51,915] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:51,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ba23fa4-b44a-47d2-9ee8-4dc14154c262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:51,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ba23fa4-b44a-47d2-9ee8-4dc14154c262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:51,916] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:51,916] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:45:51,916] [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 03:45:51,917] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3477/tc_result.tsv
[2023-03-18 03:45:51,917] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:51,917] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:51,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ba23fa4-b44a-47d2-9ee8-4dc14154c262/dqc_reference/checkm_data
[2023-03-18 03:45:51,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:51,996] [INFO] Task started: CheckM
[2023-03-18 03:45:51,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3477/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3477/checkm_input OceanDNA-b3477/checkm_result
[2023-03-18 03:46:45,749] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:45,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:45,752] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:45,752] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:45,752] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3477/markers.fasta)
[2023-03-18 03:46:45,752] [INFO] Task started: Blastn
[2023-03-18 03:46:45,753] [INFO] Running command: blastn -query OceanDNA-b3477/markers.fasta -db /var/lib/cwl/stg6ba23fa4-b44a-47d2-9ee8-4dc14154c262/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3477/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:46,437] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:46,438] [INFO] Selected 25 target genomes.
[2023-03-18 03:46:46,438] [INFO] Target genome list was writen to OceanDNA-b3477/target_genomes_gtdb.txt
[2023-03-18 03:46:46,689] [INFO] Task started: fastANI
[2023-03-18 03:46:46,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07ac0d7-e5dd-4d5b-a735-67f64380a755/OceanDNA-b3477.fa --refList OceanDNA-b3477/target_genomes_gtdb.txt --output OceanDNA-b3477/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:47:00,334] [INFO] Task succeeded: fastANI
[2023-03-18 03:47:00,338] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:47:00,339] [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_002686705.1	s__GCA-002708315 sp002686705	79.0046	435	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382445.1	s__GCA-002708315 sp014382445	77.499	269	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.88	99.88	0.96	0.96	2	-
GCA_013203805.1	s__GCA-002708315 sp013203805	76.9824	210	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845105.1	s__GCA-002708315 sp016845105	76.8099	184	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018661505.1	s__GCA-002708315 sp018661505	76.6744	87	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.95	99.92	0.97	0.96	16	-
GCA_002708315.1	s__GCA-002708315 sp002708315	75.6905	78	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:47:00,339] [INFO] GTDB search result was written to OceanDNA-b3477/result_gtdb.tsv
[2023-03-18 03:47:00,339] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:47:00,340] [INFO] DFAST_QC result json was written to OceanDNA-b3477/dqc_result.json
[2023-03-18 03:47:00,340] [INFO] DFAST_QC completed!
[2023-03-18 03:47:00,340] [INFO] Total running time: 0h1m50s