[2023-03-14 12:43:36,767] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:43:36,767] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:43:36,767] [INFO] DQC Reference Directory: /var/lib/cwl/stge80c4c2a-caf7-4753-b83a-582df5609cb8/dqc_reference
[2023-03-14 12:43:40,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:43:40,858] [INFO] Task started: Prodigal
[2023-03-14 12:43:40,858] [INFO] Running command: cat /var/lib/cwl/stgf66ecfec-675f-48f7-b83a-2e47a077cbb4/OceanDNA-b7645.fa | prodigal -d OceanDNA-b7645/cds.fna -a OceanDNA-b7645/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:43:45,825] [INFO] Task succeeded: Prodigal
[2023-03-14 12:43:45,825] [INFO] Task started: HMMsearch
[2023-03-14 12:43:45,825] [INFO] Running command: hmmsearch --tblout OceanDNA-b7645/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge80c4c2a-caf7-4753-b83a-582df5609cb8/dqc_reference/reference_markers.hmm OceanDNA-b7645/protein.faa > /dev/null
[2023-03-14 12:43:46,056] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:43:46,056] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf66ecfec-675f-48f7-b83a-2e47a077cbb4/OceanDNA-b7645.fa]
[2023-03-14 12:43:46,067] [INFO] Query marker FASTA was written to OceanDNA-b7645/markers.fasta
[2023-03-14 12:43:46,069] [INFO] Task started: Blastn
[2023-03-14 12:43:46,069] [INFO] Running command: blastn -query OceanDNA-b7645/markers.fasta -db /var/lib/cwl/stge80c4c2a-caf7-4753-b83a-582df5609cb8/dqc_reference/reference_markers.fasta -out OceanDNA-b7645/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:43:49,598] [INFO] Task succeeded: Blastn
[2023-03-14 12:43:49,600] [INFO] Selected 22 target genomes.
[2023-03-14 12:43:49,601] [INFO] Target genome list was writen to OceanDNA-b7645/target_genomes.txt
[2023-03-14 12:43:49,623] [INFO] Task started: fastANI
[2023-03-14 12:43:49,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgf66ecfec-675f-48f7-b83a-2e47a077cbb4/OceanDNA-b7645.fa --refList OceanDNA-b7645/target_genomes.txt --output OceanDNA-b7645/fastani_result.tsv --threads 1
[2023-03-14 12:44:04,771] [INFO] Task succeeded: fastANI
[2023-03-14 12:44:04,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge80c4c2a-caf7-4753-b83a-582df5609cb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:44:04,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge80c4c2a-caf7-4753-b83a-582df5609cb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:44:04,772] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:44:04,772] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:44:04,772] [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
--------------------------------------------------------------------------------
[2023-03-14 12:44:04,774] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7645/tc_result.tsv
[2023-03-14 12:44:04,774] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:44:04,774] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:44:04,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge80c4c2a-caf7-4753-b83a-582df5609cb8/dqc_reference/checkm_data
[2023-03-14 12:44:04,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:44:04,780] [INFO] Task started: CheckM
[2023-03-14 12:44:04,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7645/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7645/checkm_input OceanDNA-b7645/checkm_result
[2023-03-14 12:44:24,411] [INFO] Task succeeded: CheckM
[2023-03-14 12:44:24,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:44:24,418] [INFO] ===== Completeness check finished =====
[2023-03-14 12:44:24,418] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:44:24,418] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7645/markers.fasta)
[2023-03-14 12:44:24,418] [INFO] Task started: Blastn
[2023-03-14 12:44:24,418] [INFO] Running command: blastn -query OceanDNA-b7645/markers.fasta -db /var/lib/cwl/stge80c4c2a-caf7-4753-b83a-582df5609cb8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7645/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:44:25,691] [INFO] Task succeeded: Blastn
[2023-03-14 12:44:25,695] [INFO] Selected 19 target genomes.
[2023-03-14 12:44:25,695] [INFO] Target genome list was writen to OceanDNA-b7645/target_genomes_gtdb.txt
[2023-03-14 12:44:25,708] [INFO] Task started: fastANI
[2023-03-14 12:44:25,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgf66ecfec-675f-48f7-b83a-2e47a077cbb4/OceanDNA-b7645.fa --refList OceanDNA-b7645/target_genomes_gtdb.txt --output OceanDNA-b7645/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:44:32,351] [INFO] Task succeeded: fastANI
[2023-03-14 12:44:32,356] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:44:32,356] [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_002705485.1	s__MAG-121220-bin8 sp002705485	85.6027	181	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.79	97.60	0.73	0.71	4	-
GCA_902523635.1	s__MAG-121220-bin8 sp902523635	77.614	96	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	77.3997	78	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	77.2576	61	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	76.9555	91	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	76.8593	72	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	76.5883	79	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	76.4354	57	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:44:32,358] [INFO] GTDB search result was written to OceanDNA-b7645/result_gtdb.tsv
[2023-03-14 12:44:32,358] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:44:32,360] [INFO] DFAST_QC result json was written to OceanDNA-b7645/dqc_result.json
[2023-03-14 12:44:32,360] [INFO] DFAST_QC completed!
[2023-03-14 12:44:32,360] [INFO] Total running time: 0h0m56s