[2023-03-16 22:45:35,371] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:45:35,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:45:35,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg98a30b18-b325-439b-b552-fd141565aa2a/dqc_reference
[2023-03-16 22:45:37,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:45:37,282] [INFO] Task started: Prodigal
[2023-03-16 22:45:37,282] [INFO] Running command: cat /var/lib/cwl/stgc76600a4-304d-49a2-99b5-e3f74caa9a95/OceanDNA-b7106.fa | prodigal -d OceanDNA-b7106/cds.fna -a OceanDNA-b7106/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:45:45,199] [INFO] Task succeeded: Prodigal
[2023-03-16 22:45:45,199] [INFO] Task started: HMMsearch
[2023-03-16 22:45:45,199] [INFO] Running command: hmmsearch --tblout OceanDNA-b7106/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98a30b18-b325-439b-b552-fd141565aa2a/dqc_reference/reference_markers.hmm OceanDNA-b7106/protein.faa > /dev/null
[2023-03-16 22:45:45,390] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:45:45,390] [INFO] Found 6/6 markers.
[2023-03-16 22:45:45,402] [INFO] Query marker FASTA was written to OceanDNA-b7106/markers.fasta
[2023-03-16 22:45:45,402] [INFO] Task started: Blastn
[2023-03-16 22:45:45,402] [INFO] Running command: blastn -query OceanDNA-b7106/markers.fasta -db /var/lib/cwl/stg98a30b18-b325-439b-b552-fd141565aa2a/dqc_reference/reference_markers.fasta -out OceanDNA-b7106/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:45:45,979] [INFO] Task succeeded: Blastn
[2023-03-16 22:45:45,980] [INFO] Selected 30 target genomes.
[2023-03-16 22:45:45,981] [INFO] Target genome list was writen to OceanDNA-b7106/target_genomes.txt
[2023-03-16 22:45:45,996] [INFO] Task started: fastANI
[2023-03-16 22:45:45,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgc76600a4-304d-49a2-99b5-e3f74caa9a95/OceanDNA-b7106.fa --refList OceanDNA-b7106/target_genomes.txt --output OceanDNA-b7106/fastani_result.tsv --threads 1
[2023-03-16 22:46:01,829] [INFO] Task succeeded: fastANI
[2023-03-16 22:46:01,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98a30b18-b325-439b-b552-fd141565aa2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:46:01,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98a30b18-b325-439b-b552-fd141565aa2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:46:01,829] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 22:46:01,830] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 22:46:01,830] [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
--------------------------------------------------------------------------------
[2023-03-16 22:46:01,830] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7106/tc_result.tsv
[2023-03-16 22:46:01,830] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:46:01,830] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:46:01,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98a30b18-b325-439b-b552-fd141565aa2a/dqc_reference/checkm_data
[2023-03-16 22:46:01,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:46:01,835] [INFO] Task started: CheckM
[2023-03-16 22:46:01,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7106/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7106/checkm_input OceanDNA-b7106/checkm_result
[2023-03-16 22:46:26,532] [INFO] Task succeeded: CheckM
[2023-03-16 22:46:26,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 22:46:26,534] [INFO] ===== Completeness check finished =====
[2023-03-16 22:46:26,534] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:46:26,534] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7106/markers.fasta)
[2023-03-16 22:46:26,536] [INFO] Task started: Blastn
[2023-03-16 22:46:26,536] [INFO] Running command: blastn -query OceanDNA-b7106/markers.fasta -db /var/lib/cwl/stg98a30b18-b325-439b-b552-fd141565aa2a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7106/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:46:27,502] [INFO] Task succeeded: Blastn
[2023-03-16 22:46:27,503] [INFO] Selected 14 target genomes.
[2023-03-16 22:46:27,503] [INFO] Target genome list was writen to OceanDNA-b7106/target_genomes_gtdb.txt
[2023-03-16 22:46:28,016] [INFO] Task started: fastANI
[2023-03-16 22:46:28,016] [INFO] Running command: fastANI --query /var/lib/cwl/stgc76600a4-304d-49a2-99b5-e3f74caa9a95/OceanDNA-b7106.fa --refList OceanDNA-b7106/target_genomes_gtdb.txt --output OceanDNA-b7106/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:46:31,611] [INFO] Task succeeded: fastANI
[2023-03-16 22:46:31,619] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 22:46:31,619] [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_002700405.1	s__GCA-2700405 sp002700405	98.4127	299	433	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902512065.1	s__GCA-2700405 sp902512065	92.0427	301	433	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	91.5735	292	433	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_014239895.1	s__GCA-2700405 sp014239895	82.1189	231	433	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_018657955.1	s__GCA-2700405 sp018657955	81.9483	318	433	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	99.95	99.87	0.95	0.89	9	-
GCA_002697255.1	s__MED-G13 sp002697255	78.052	90	433	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_902510415.1	s__MED-G13 sp902510415	77.8505	86	433	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_902604715.1	s__MED-G13 sp902604715	77.0227	69	433	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.66	97.66	0.81	0.81	2	-
GCA_902510475.1	s__MED-G13 sp902510475	76.794	73	433	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_902518355.1	s__MED-G13 sp902518355	76.6734	81	433	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_902509675.1	s__MED-G13 sp902509675	76.6538	62	433	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	76.5331	77	433	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_902526075.1	s__MED-G13 sp902526075	76.5232	68	433	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 22:46:31,619] [INFO] GTDB search result was written to OceanDNA-b7106/result_gtdb.tsv
[2023-03-16 22:46:31,619] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:46:31,620] [INFO] DFAST_QC result json was written to OceanDNA-b7106/dqc_result.json
[2023-03-16 22:46:31,620] [INFO] DFAST_QC completed!
[2023-03-16 22:46:31,620] [INFO] Total running time: 0h0m56s