[2023-03-19 03:10:00,710] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,710] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg73f3f178-31d5-42de-b645-5d923d253c89/dqc_reference
[2023-03-19 03:10:01,799] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,800] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,800] [INFO] Running command: cat /var/lib/cwl/stg23577207-8d79-4039-a4ad-831a23a3bd04/OceanDNA-b11934.fa | prodigal -d OceanDNA-b11934/cds.fna -a OceanDNA-b11934/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:15,980] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:15,980] [INFO] Task started: HMMsearch
[2023-03-19 03:10:15,980] [INFO] Running command: hmmsearch --tblout OceanDNA-b11934/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73f3f178-31d5-42de-b645-5d923d253c89/dqc_reference/reference_markers.hmm OceanDNA-b11934/protein.faa > /dev/null
[2023-03-19 03:10:16,123] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:16,124] [INFO] Found 6/6 markers.
[2023-03-19 03:10:16,137] [INFO] Query marker FASTA was written to OceanDNA-b11934/markers.fasta
[2023-03-19 03:10:16,137] [INFO] Task started: Blastn
[2023-03-19 03:10:16,137] [INFO] Running command: blastn -query OceanDNA-b11934/markers.fasta -db /var/lib/cwl/stg73f3f178-31d5-42de-b645-5d923d253c89/dqc_reference/reference_markers.fasta -out OceanDNA-b11934/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:16,669] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:16,670] [INFO] Selected 30 target genomes.
[2023-03-19 03:10:16,670] [INFO] Target genome list was writen to OceanDNA-b11934/target_genomes.txt
[2023-03-19 03:10:16,686] [INFO] Task started: fastANI
[2023-03-19 03:10:16,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg23577207-8d79-4039-a4ad-831a23a3bd04/OceanDNA-b11934.fa --refList OceanDNA-b11934/target_genomes.txt --output OceanDNA-b11934/fastani_result.tsv --threads 1
[2023-03-19 03:10:35,160] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:35,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73f3f178-31d5-42de-b645-5d923d253c89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:35,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73f3f178-31d5-42de-b645-5d923d253c89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:35,161] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:35,161] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:10:35,161] [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 03:10:35,161] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11934/tc_result.tsv
[2023-03-19 03:10:35,161] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:35,161] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:35,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73f3f178-31d5-42de-b645-5d923d253c89/dqc_reference/checkm_data
[2023-03-19 03:10:35,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:35,169] [INFO] Task started: CheckM
[2023-03-19 03:10:35,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11934/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11934/checkm_input OceanDNA-b11934/checkm_result
[2023-03-19 03:11:14,686] [INFO] Task succeeded: CheckM
[2023-03-19 03:11:14,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.15%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 03:11:14,689] [INFO] ===== Completeness check finished =====
[2023-03-19 03:11:14,689] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:11:14,689] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11934/markers.fasta)
[2023-03-19 03:11:14,690] [INFO] Task started: Blastn
[2023-03-19 03:11:14,690] [INFO] Running command: blastn -query OceanDNA-b11934/markers.fasta -db /var/lib/cwl/stg73f3f178-31d5-42de-b645-5d923d253c89/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11934/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:11:15,479] [INFO] Task succeeded: Blastn
[2023-03-19 03:11:15,480] [INFO] Selected 14 target genomes.
[2023-03-19 03:11:15,480] [INFO] Target genome list was writen to OceanDNA-b11934/target_genomes_gtdb.txt
[2023-03-19 03:11:15,538] [INFO] Task started: fastANI
[2023-03-19 03:11:15,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg23577207-8d79-4039-a4ad-831a23a3bd04/OceanDNA-b11934.fa --refList OceanDNA-b11934/target_genomes_gtdb.txt --output OceanDNA-b11934/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:11:20,770] [INFO] Task succeeded: fastANI
[2023-03-19 03:11:20,774] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:11:20,774] [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_002729115.1	s__UBA11663 sp002729115	98.6064	168	195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	96.51	95.05	0.71	0.69	4	conclusive
GCA_002469765.1	s__UBA11663 sp002469765	84.8318	171	195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683345.1	s__UBA11663 sp002683345	79.4158	76	195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524845.1	s__UBA11663 sp011524845	79.2597	79	195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863145.1	s__UBA11663 sp002863145	79.2492	101	195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
--------------------------------------------------------------------------------
[2023-03-19 03:11:20,775] [INFO] GTDB search result was written to OceanDNA-b11934/result_gtdb.tsv
[2023-03-19 03:11:20,775] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:11:20,776] [INFO] DFAST_QC result json was written to OceanDNA-b11934/dqc_result.json
[2023-03-19 03:11:20,776] [INFO] DFAST_QC completed!
[2023-03-19 03:11:20,776] [INFO] Total running time: 0h1m20s