[2023-03-14 11:36:02,661] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:36:02,661] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:36:02,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg96c59299-3f0c-4bfa-882e-18eeb6cd0bdf/dqc_reference
[2023-03-14 11:36:04,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:36:04,406] [INFO] Task started: Prodigal
[2023-03-14 11:36:04,407] [INFO] Running command: cat /var/lib/cwl/stg811c40cd-cafe-4384-b540-ed44d98ccb00/OceanDNA-b8895.fa | prodigal -d OceanDNA-b8895/cds.fna -a OceanDNA-b8895/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:36:08,194] [INFO] Task succeeded: Prodigal
[2023-03-14 11:36:08,194] [INFO] Task started: HMMsearch
[2023-03-14 11:36:08,194] [INFO] Running command: hmmsearch --tblout OceanDNA-b8895/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96c59299-3f0c-4bfa-882e-18eeb6cd0bdf/dqc_reference/reference_markers.hmm OceanDNA-b8895/protein.faa > /dev/null
[2023-03-14 11:36:08,349] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:36:08,349] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg811c40cd-cafe-4384-b540-ed44d98ccb00/OceanDNA-b8895.fa]
[2023-03-14 11:36:08,358] [INFO] Query marker FASTA was written to OceanDNA-b8895/markers.fasta
[2023-03-14 11:36:08,359] [INFO] Task started: Blastn
[2023-03-14 11:36:08,359] [INFO] Running command: blastn -query OceanDNA-b8895/markers.fasta -db /var/lib/cwl/stg96c59299-3f0c-4bfa-882e-18eeb6cd0bdf/dqc_reference/reference_markers.fasta -out OceanDNA-b8895/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:10,017] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:10,018] [INFO] Selected 18 target genomes.
[2023-03-14 11:36:10,018] [INFO] Target genome list was writen to OceanDNA-b8895/target_genomes.txt
[2023-03-14 11:36:10,031] [INFO] Task started: fastANI
[2023-03-14 11:36:10,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg811c40cd-cafe-4384-b540-ed44d98ccb00/OceanDNA-b8895.fa --refList OceanDNA-b8895/target_genomes.txt --output OceanDNA-b8895/fastani_result.tsv --threads 1
[2023-03-14 11:36:19,969] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:19,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96c59299-3f0c-4bfa-882e-18eeb6cd0bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:36:19,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96c59299-3f0c-4bfa-882e-18eeb6cd0bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:36:19,970] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:36:19,970] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:36:19,970] [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 11:36:19,971] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8895/tc_result.tsv
[2023-03-14 11:36:19,971] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:36:19,971] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:36:19,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96c59299-3f0c-4bfa-882e-18eeb6cd0bdf/dqc_reference/checkm_data
[2023-03-14 11:36:19,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:36:19,977] [INFO] Task started: CheckM
[2023-03-14 11:36:19,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8895/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8895/checkm_input OceanDNA-b8895/checkm_result
[2023-03-14 11:36:36,048] [INFO] Task succeeded: CheckM
[2023-03-14 11:36:36,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.85%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:36:36,050] [INFO] ===== Completeness check finished =====
[2023-03-14 11:36:36,050] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:36:36,050] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8895/markers.fasta)
[2023-03-14 11:36:36,050] [INFO] Task started: Blastn
[2023-03-14 11:36:36,050] [INFO] Running command: blastn -query OceanDNA-b8895/markers.fasta -db /var/lib/cwl/stg96c59299-3f0c-4bfa-882e-18eeb6cd0bdf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8895/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:36,490] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:36,491] [INFO] Selected 9 target genomes.
[2023-03-14 11:36:36,491] [INFO] Target genome list was writen to OceanDNA-b8895/target_genomes_gtdb.txt
[2023-03-14 11:36:36,567] [INFO] Task started: fastANI
[2023-03-14 11:36:36,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg811c40cd-cafe-4384-b540-ed44d98ccb00/OceanDNA-b8895.fa --refList OceanDNA-b8895/target_genomes_gtdb.txt --output OceanDNA-b8895/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:36:38,398] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:38,404] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:36:38,404] [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_902595555.1	s__MED-G14 sp902595555	94.1881	181	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.27	95.29	0.86	0.83	8	-
GCA_902574335.1	s__MED-G14 sp902574335	93.7104	99	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622575.1	s__MED-G14 sp902622575	82.0802	132	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515405.1	s__MED-G14 sp902515405	79.8952	106	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331885.1	s__MED-G14 sp003331885	79.4567	85	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.85	96.85	0.80	0.80	2	-
GCA_902546095.1	s__MED-G14 sp902546095	79.3814	100	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606555.1	s__MED-G14 sp902606555	79.2706	70	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902535165.1	s__MED-G14 sp902535165	79.2253	117	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597545.1	s__MED-G14 sp902597545	79.0251	134	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.96	95.61	0.87	0.83	5	-
--------------------------------------------------------------------------------
[2023-03-14 11:36:38,405] [INFO] GTDB search result was written to OceanDNA-b8895/result_gtdb.tsv
[2023-03-14 11:36:38,405] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:36:38,406] [INFO] DFAST_QC result json was written to OceanDNA-b8895/dqc_result.json
[2023-03-14 11:36:38,406] [INFO] DFAST_QC completed!
[2023-03-14 11:36:38,406] [INFO] Total running time: 0h0m36s