[2023-03-17 05:54:59,365] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:54:59,365] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:54:59,365] [INFO] DQC Reference Directory: /var/lib/cwl/stgabb886db-31f5-4c13-93b9-a00cbd79c279/dqc_reference
[2023-03-17 05:55:01,031] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:55:01,033] [INFO] Task started: Prodigal
[2023-03-17 05:55:01,033] [INFO] Running command: cat /var/lib/cwl/stgdce9e82d-2775-4a5b-8aff-0fe12b12e954/OceanDNA-b11673.fa | prodigal -d OceanDNA-b11673/cds.fna -a OceanDNA-b11673/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:55:20,112] [INFO] Task succeeded: Prodigal
[2023-03-17 05:55:20,112] [INFO] Task started: HMMsearch
[2023-03-17 05:55:20,112] [INFO] Running command: hmmsearch --tblout OceanDNA-b11673/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabb886db-31f5-4c13-93b9-a00cbd79c279/dqc_reference/reference_markers.hmm OceanDNA-b11673/protein.faa > /dev/null
[2023-03-17 05:55:20,276] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:55:20,277] [INFO] Found 6/6 markers.
[2023-03-17 05:55:20,294] [INFO] Query marker FASTA was written to OceanDNA-b11673/markers.fasta
[2023-03-17 05:55:20,295] [INFO] Task started: Blastn
[2023-03-17 05:55:20,295] [INFO] Running command: blastn -query OceanDNA-b11673/markers.fasta -db /var/lib/cwl/stgabb886db-31f5-4c13-93b9-a00cbd79c279/dqc_reference/reference_markers.fasta -out OceanDNA-b11673/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:55:20,823] [INFO] Task succeeded: Blastn
[2023-03-17 05:55:20,828] [INFO] Selected 32 target genomes.
[2023-03-17 05:55:20,828] [INFO] Target genome list was writen to OceanDNA-b11673/target_genomes.txt
[2023-03-17 05:55:20,843] [INFO] Task started: fastANI
[2023-03-17 05:55:20,843] [INFO] Running command: fastANI --query /var/lib/cwl/stgdce9e82d-2775-4a5b-8aff-0fe12b12e954/OceanDNA-b11673.fa --refList OceanDNA-b11673/target_genomes.txt --output OceanDNA-b11673/fastani_result.tsv --threads 1
[2023-03-17 05:55:42,790] [INFO] Task succeeded: fastANI
[2023-03-17 05:55:42,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabb886db-31f5-4c13-93b9-a00cbd79c279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:55:42,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabb886db-31f5-4c13-93b9-a00cbd79c279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:55:42,791] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:55:42,791] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:55:42,791] [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 05:55:42,803] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11673/tc_result.tsv
[2023-03-17 05:55:42,804] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:55:42,804] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:55:42,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabb886db-31f5-4c13-93b9-a00cbd79c279/dqc_reference/checkm_data
[2023-03-17 05:55:42,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:55:42,810] [INFO] Task started: CheckM
[2023-03-17 05:55:42,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11673/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11673/checkm_input OceanDNA-b11673/checkm_result
[2023-03-17 05:56:33,450] [INFO] Task succeeded: CheckM
[2023-03-17 05:56:33,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:56:33,489] [INFO] ===== Completeness check finished =====
[2023-03-17 05:56:33,489] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:56:33,490] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11673/markers.fasta)
[2023-03-17 05:56:33,491] [INFO] Task started: Blastn
[2023-03-17 05:56:33,491] [INFO] Running command: blastn -query OceanDNA-b11673/markers.fasta -db /var/lib/cwl/stgabb886db-31f5-4c13-93b9-a00cbd79c279/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11673/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:56:34,231] [INFO] Task succeeded: Blastn
[2023-03-17 05:56:34,264] [INFO] Selected 21 target genomes.
[2023-03-17 05:56:34,264] [INFO] Target genome list was writen to OceanDNA-b11673/target_genomes_gtdb.txt
[2023-03-17 05:56:34,293] [INFO] Task started: fastANI
[2023-03-17 05:56:34,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgdce9e82d-2775-4a5b-8aff-0fe12b12e954/OceanDNA-b11673.fa --refList OceanDNA-b11673/target_genomes_gtdb.txt --output OceanDNA-b11673/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:56:42,917] [INFO] Task succeeded: fastANI
[2023-03-17 05:56:42,922] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:56:42,922] [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_002863125.1	s__UA16 sp002863125	85.0098	505	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	97.01	95.79	0.91	0.89	5	-
GCA_002448555.1	s__UA16 sp002448555	84.6337	429	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.35	99.35	0.96	0.96	2	-
GCA_002690915.1	s__UA16 sp002690915	80.8607	387	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	96.97	96.97	0.71	0.71	2	-
GCA_002420235.1	s__UA16 sp002420235	78.3089	234	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.27	97.82	0.87	0.83	4	-
GCA_016777435.1	s__UA16 sp016777435	76.96	60	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002323795.1	s__UA16 sp002323795	76.863	60	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.84	99.84	0.86	0.86	2	-
GCA_002292325.1	s__UA16 sp002292325	76.7741	73	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863145.1	s__UBA11663 sp002863145	76.0463	55	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
--------------------------------------------------------------------------------
[2023-03-17 05:56:42,923] [INFO] GTDB search result was written to OceanDNA-b11673/result_gtdb.tsv
[2023-03-17 05:56:42,923] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:56:42,923] [INFO] DFAST_QC result json was written to OceanDNA-b11673/dqc_result.json
[2023-03-17 05:56:42,923] [INFO] DFAST_QC completed!
[2023-03-17 05:56:42,924] [INFO] Total running time: 0h1m44s