[2023-03-15 13:03:53,435] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg4317b358-489d-4507-bc85-1487c21d5c45/dqc_reference
[2023-03-15 13:03:54,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,616] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,616] [INFO] Running command: cat /var/lib/cwl/stge242d88a-eaf9-4975-ace3-d0eaf19fcec2/OceanDNA-b12028.fa | prodigal -d OceanDNA-b12028/cds.fna -a OceanDNA-b12028/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:10,263] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:10,263] [INFO] Task started: HMMsearch
[2023-03-15 13:04:10,263] [INFO] Running command: hmmsearch --tblout OceanDNA-b12028/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4317b358-489d-4507-bc85-1487c21d5c45/dqc_reference/reference_markers.hmm OceanDNA-b12028/protein.faa > /dev/null
[2023-03-15 13:04:10,447] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:10,447] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge242d88a-eaf9-4975-ace3-d0eaf19fcec2/OceanDNA-b12028.fa]
[2023-03-15 13:04:10,461] [INFO] Query marker FASTA was written to OceanDNA-b12028/markers.fasta
[2023-03-15 13:04:10,461] [INFO] Task started: Blastn
[2023-03-15 13:04:10,461] [INFO] Running command: blastn -query OceanDNA-b12028/markers.fasta -db /var/lib/cwl/stg4317b358-489d-4507-bc85-1487c21d5c45/dqc_reference/reference_markers.fasta -out OceanDNA-b12028/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:11,023] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:11,024] [INFO] Selected 19 target genomes.
[2023-03-15 13:04:11,024] [INFO] Target genome list was writen to OceanDNA-b12028/target_genomes.txt
[2023-03-15 13:04:11,034] [INFO] Task started: fastANI
[2023-03-15 13:04:11,034] [INFO] Running command: fastANI --query /var/lib/cwl/stge242d88a-eaf9-4975-ace3-d0eaf19fcec2/OceanDNA-b12028.fa --refList OceanDNA-b12028/target_genomes.txt --output OceanDNA-b12028/fastani_result.tsv --threads 1
[2023-03-15 13:04:22,393] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:22,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4317b358-489d-4507-bc85-1487c21d5c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:22,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4317b358-489d-4507-bc85-1487c21d5c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:22,394] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:22,394] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:04:22,394] [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
--------------------------------------------------------------------------------
[2023-03-15 13:04:22,394] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12028/tc_result.tsv
[2023-03-15 13:04:22,394] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:22,394] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:22,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4317b358-489d-4507-bc85-1487c21d5c45/dqc_reference/checkm_data
[2023-03-15 13:04:22,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:22,401] [INFO] Task started: CheckM
[2023-03-15 13:04:22,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12028/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12028/checkm_input OceanDNA-b12028/checkm_result
[2023-03-15 13:05:05,510] [INFO] Task succeeded: CheckM
[2023-03-15 13:05:05,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:05:05,513] [INFO] ===== Completeness check finished =====
[2023-03-15 13:05:05,513] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:05:05,513] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12028/markers.fasta)
[2023-03-15 13:05:05,514] [INFO] Task started: Blastn
[2023-03-15 13:05:05,514] [INFO] Running command: blastn -query OceanDNA-b12028/markers.fasta -db /var/lib/cwl/stg4317b358-489d-4507-bc85-1487c21d5c45/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12028/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:05:06,232] [INFO] Task succeeded: Blastn
[2023-03-15 13:05:06,233] [INFO] Selected 16 target genomes.
[2023-03-15 13:05:06,234] [INFO] Target genome list was writen to OceanDNA-b12028/target_genomes_gtdb.txt
[2023-03-15 13:05:06,318] [INFO] Task started: fastANI
[2023-03-15 13:05:06,318] [INFO] Running command: fastANI --query /var/lib/cwl/stge242d88a-eaf9-4975-ace3-d0eaf19fcec2/OceanDNA-b12028.fa --refList OceanDNA-b12028/target_genomes_gtdb.txt --output OceanDNA-b12028/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:05:13,279] [INFO] Task succeeded: fastANI
[2023-03-15 13:05:13,284] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:05:13,284] [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_905480095.1	s__UBA974 sp905480095	98.7475	525	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002700285.1	s__UBA974 sp002700285	92.7739	612	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	99.89	99.89	0.95	0.95	2	-
GCA_002336655.1	s__UBA974 sp002336655	89.0079	480	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700255.1	s__UBA974 sp018700255	77.8708	91	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660615.1	s__UBA974 sp015660615	77.7841	81	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339135.1	s__UBA974 sp002339135	77.4163	100	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746975.1	s__UBA974 sp002746975	77.1648	111	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:05:13,285] [INFO] GTDB search result was written to OceanDNA-b12028/result_gtdb.tsv
[2023-03-15 13:05:13,285] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:05:13,286] [INFO] DFAST_QC result json was written to OceanDNA-b12028/dqc_result.json
[2023-03-15 13:05:13,286] [INFO] DFAST_QC completed!
[2023-03-15 13:05:13,286] [INFO] Total running time: 0h1m20s