[2023-03-15 08:09:45,465] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,466] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg15830e24-b28c-4b1b-aaf2-78199b6ee0e6/dqc_reference
[2023-03-15 08:09:46,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,633] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,633] [INFO] Running command: cat /var/lib/cwl/stg383b2e9b-0a60-4ce8-87bd-3fb7618f3d6f/OceanDNA-b7075.fa | prodigal -d OceanDNA-b7075/cds.fna -a OceanDNA-b7075/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:55,275] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:55,275] [INFO] Task started: HMMsearch
[2023-03-15 08:09:55,275] [INFO] Running command: hmmsearch --tblout OceanDNA-b7075/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15830e24-b28c-4b1b-aaf2-78199b6ee0e6/dqc_reference/reference_markers.hmm OceanDNA-b7075/protein.faa > /dev/null
[2023-03-15 08:09:55,478] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:55,479] [INFO] Found 6/6 markers.
[2023-03-15 08:09:55,489] [INFO] Query marker FASTA was written to OceanDNA-b7075/markers.fasta
[2023-03-15 08:09:55,490] [INFO] Task started: Blastn
[2023-03-15 08:09:55,490] [INFO] Running command: blastn -query OceanDNA-b7075/markers.fasta -db /var/lib/cwl/stg15830e24-b28c-4b1b-aaf2-78199b6ee0e6/dqc_reference/reference_markers.fasta -out OceanDNA-b7075/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:09:56,080] [INFO] Task succeeded: Blastn
[2023-03-15 08:09:56,081] [INFO] Selected 30 target genomes.
[2023-03-15 08:09:56,081] [INFO] Target genome list was writen to OceanDNA-b7075/target_genomes.txt
[2023-03-15 08:09:56,093] [INFO] Task started: fastANI
[2023-03-15 08:09:56,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg383b2e9b-0a60-4ce8-87bd-3fb7618f3d6f/OceanDNA-b7075.fa --refList OceanDNA-b7075/target_genomes.txt --output OceanDNA-b7075/fastani_result.tsv --threads 1
[2023-03-15 08:10:13,039] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:13,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15830e24-b28c-4b1b-aaf2-78199b6ee0e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:13,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15830e24-b28c-4b1b-aaf2-78199b6ee0e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:13,040] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:13,040] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:10:13,040] [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
--------------------------------------------------------------------------------
[2023-03-15 08:10:13,040] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7075/tc_result.tsv
[2023-03-15 08:10:13,040] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:13,040] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:13,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15830e24-b28c-4b1b-aaf2-78199b6ee0e6/dqc_reference/checkm_data
[2023-03-15 08:10:13,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:13,049] [INFO] Task started: CheckM
[2023-03-15 08:10:13,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7075/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7075/checkm_input OceanDNA-b7075/checkm_result
[2023-03-15 08:10:39,359] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:39,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:39,362] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:39,362] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:39,362] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7075/markers.fasta)
[2023-03-15 08:10:39,362] [INFO] Task started: Blastn
[2023-03-15 08:10:39,362] [INFO] Running command: blastn -query OceanDNA-b7075/markers.fasta -db /var/lib/cwl/stg15830e24-b28c-4b1b-aaf2-78199b6ee0e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7075/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:40,328] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:40,329] [INFO] Selected 16 target genomes.
[2023-03-15 08:10:40,329] [INFO] Target genome list was writen to OceanDNA-b7075/target_genomes_gtdb.txt
[2023-03-15 08:10:40,343] [INFO] Task started: fastANI
[2023-03-15 08:10:40,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg383b2e9b-0a60-4ce8-87bd-3fb7618f3d6f/OceanDNA-b7075.fa --refList OceanDNA-b7075/target_genomes_gtdb.txt --output OceanDNA-b7075/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:45,255] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:45,263] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:10:45,264] [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_018657955.1	s__GCA-2700405 sp018657955	99.9117	462	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	99.95	99.87	0.95	0.89	9	conclusive
GCA_014239895.1	s__GCA-2700405 sp014239895	90.3764	271	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512065.1	s__GCA-2700405 sp902512065	82.6612	316	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213965.1	s__GCA-2700405 sp004213965	82.1376	270	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700405.1	s__GCA-2700405 sp002700405	81.6941	256	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510415.1	s__MED-G13 sp902510415	76.9981	73	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_902608795.1	s__MED-G13 sp902608795	76.935	66	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515565.1	s__SGZJ01 sp902515565	76.8591	78	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697255.1	s__MED-G13 sp002697255	76.8335	93	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526075.1	s__MED-G13 sp902526075	76.6905	70	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691265.1	s__MED-G13 sp002691265	76.4132	78	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.61	95.49	0.82	0.79	4	-
GCA_902581145.1	s__MED-G13 sp902581145	76.4022	80	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674025.1	s__SGZJ01 sp018674025	76.043	67	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:45,264] [INFO] GTDB search result was written to OceanDNA-b7075/result_gtdb.tsv
[2023-03-15 08:10:45,265] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:45,267] [INFO] DFAST_QC result json was written to OceanDNA-b7075/dqc_result.json
[2023-03-15 08:10:45,267] [INFO] DFAST_QC completed!
[2023-03-15 08:10:45,267] [INFO] Total running time: 0h0m60s