[2023-03-19 00:01:03,327] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,327] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg5db43460-c2d5-4a99-b497-6b3603409fcf/dqc_reference
[2023-03-19 00:01:04,643] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,643] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,644] [INFO] Running command: cat /var/lib/cwl/stga95242b8-f292-4404-b867-a53e3e9cfc2e/OceanDNA-b5422.fa | prodigal -d OceanDNA-b5422/cds.fna -a OceanDNA-b5422/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:13,561] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:13,562] [INFO] Task started: HMMsearch
[2023-03-19 00:01:13,562] [INFO] Running command: hmmsearch --tblout OceanDNA-b5422/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5db43460-c2d5-4a99-b497-6b3603409fcf/dqc_reference/reference_markers.hmm OceanDNA-b5422/protein.faa > /dev/null
[2023-03-19 00:01:13,790] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:13,791] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga95242b8-f292-4404-b867-a53e3e9cfc2e/OceanDNA-b5422.fa]
[2023-03-19 00:01:13,803] [INFO] Query marker FASTA was written to OceanDNA-b5422/markers.fasta
[2023-03-19 00:01:13,803] [INFO] Task started: Blastn
[2023-03-19 00:01:13,803] [INFO] Running command: blastn -query OceanDNA-b5422/markers.fasta -db /var/lib/cwl/stg5db43460-c2d5-4a99-b497-6b3603409fcf/dqc_reference/reference_markers.fasta -out OceanDNA-b5422/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:14,330] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:14,331] [INFO] Selected 19 target genomes.
[2023-03-19 00:01:14,331] [INFO] Target genome list was writen to OceanDNA-b5422/target_genomes.txt
[2023-03-19 00:01:14,340] [INFO] Task started: fastANI
[2023-03-19 00:01:14,341] [INFO] Running command: fastANI --query /var/lib/cwl/stga95242b8-f292-4404-b867-a53e3e9cfc2e/OceanDNA-b5422.fa --refList OceanDNA-b5422/target_genomes.txt --output OceanDNA-b5422/fastani_result.tsv --threads 1
[2023-03-19 00:01:25,163] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:25,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5db43460-c2d5-4a99-b497-6b3603409fcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:25,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5db43460-c2d5-4a99-b497-6b3603409fcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:25,164] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:25,164] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:01:25,164] [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 00:01:25,164] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5422/tc_result.tsv
[2023-03-19 00:01:25,164] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:25,165] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:25,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5db43460-c2d5-4a99-b497-6b3603409fcf/dqc_reference/checkm_data
[2023-03-19 00:01:25,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:25,171] [INFO] Task started: CheckM
[2023-03-19 00:01:25,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5422/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5422/checkm_input OceanDNA-b5422/checkm_result
[2023-03-19 00:01:52,706] [INFO] Task succeeded: CheckM
[2023-03-19 00:01:52,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.89%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 00:01:52,709] [INFO] ===== Completeness check finished =====
[2023-03-19 00:01:52,709] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:01:52,709] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5422/markers.fasta)
[2023-03-19 00:01:52,710] [INFO] Task started: Blastn
[2023-03-19 00:01:52,710] [INFO] Running command: blastn -query OceanDNA-b5422/markers.fasta -db /var/lib/cwl/stg5db43460-c2d5-4a99-b497-6b3603409fcf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5422/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:53,420] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:53,421] [INFO] Selected 19 target genomes.
[2023-03-19 00:01:53,421] [INFO] Target genome list was writen to OceanDNA-b5422/target_genomes_gtdb.txt
[2023-03-19 00:01:53,447] [INFO] Task started: fastANI
[2023-03-19 00:01:53,447] [INFO] Running command: fastANI --query /var/lib/cwl/stga95242b8-f292-4404-b867-a53e3e9cfc2e/OceanDNA-b5422.fa --refList OceanDNA-b5422/target_genomes_gtdb.txt --output OceanDNA-b5422/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:02,162] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:02,166] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:02:02,167] [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_009926125.1	s__UBA952 sp009926125	91.6647	229	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923965.1	s__UBA952 sp009923965	89.7829	199	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798205.1	s__UBA952 sp005798205	79.6456	110	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883325.1	s__UBA952 sp018883325	76.575	82	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903939755.1	s__UBA952 sp903939755	76.3317	60	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.13	98.32	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:02,167] [INFO] GTDB search result was written to OceanDNA-b5422/result_gtdb.tsv
[2023-03-19 00:02:02,167] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:02,168] [INFO] DFAST_QC result json was written to OceanDNA-b5422/dqc_result.json
[2023-03-19 00:02:02,168] [INFO] DFAST_QC completed!
[2023-03-19 00:02:02,168] [INFO] Total running time: 0h0m59s