[2023-03-14 14:52:56,706] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:52:56,706] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:52:56,707] [INFO] DQC Reference Directory: /var/lib/cwl/stgfef3f9e5-b26e-420e-9865-6832df3e30e8/dqc_reference
[2023-03-14 14:52:58,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:52:58,826] [INFO] Task started: Prodigal
[2023-03-14 14:52:58,826] [INFO] Running command: cat /var/lib/cwl/stg2a78878d-c9af-4bbb-9b2a-e89653137c08/OceanDNA-b12633.fa | prodigal -d OceanDNA-b12633/cds.fna -a OceanDNA-b12633/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:53:25,538] [INFO] Task succeeded: Prodigal
[2023-03-14 14:53:25,538] [INFO] Task started: HMMsearch
[2023-03-14 14:53:25,538] [INFO] Running command: hmmsearch --tblout OceanDNA-b12633/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfef3f9e5-b26e-420e-9865-6832df3e30e8/dqc_reference/reference_markers.hmm OceanDNA-b12633/protein.faa > /dev/null
[2023-03-14 14:53:25,726] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:53:25,726] [INFO] Found 6/6 markers.
[2023-03-14 14:53:25,746] [INFO] Query marker FASTA was written to OceanDNA-b12633/markers.fasta
[2023-03-14 14:53:25,748] [INFO] Task started: Blastn
[2023-03-14 14:53:25,748] [INFO] Running command: blastn -query OceanDNA-b12633/markers.fasta -db /var/lib/cwl/stgfef3f9e5-b26e-420e-9865-6832df3e30e8/dqc_reference/reference_markers.fasta -out OceanDNA-b12633/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:53:26,373] [INFO] Task succeeded: Blastn
[2023-03-14 14:53:26,373] [INFO] Selected 29 target genomes.
[2023-03-14 14:53:26,374] [INFO] Target genome list was writen to OceanDNA-b12633/target_genomes.txt
[2023-03-14 14:53:26,384] [INFO] Task started: fastANI
[2023-03-14 14:53:26,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a78878d-c9af-4bbb-9b2a-e89653137c08/OceanDNA-b12633.fa --refList OceanDNA-b12633/target_genomes.txt --output OceanDNA-b12633/fastani_result.tsv --threads 1
[2023-03-14 14:53:42,962] [INFO] Task succeeded: fastANI
[2023-03-14 14:53:42,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfef3f9e5-b26e-420e-9865-6832df3e30e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:53:42,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfef3f9e5-b26e-420e-9865-6832df3e30e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:53:42,969] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:53:42,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:53:42,969] [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
Vicingus serpentipes	strain=NCIMB 15042	GCA_007993035.1	1926625	1926625	type	True	77.001	209	999	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	75.3466	75	999	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	75.3339	76	999	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	75.3216	77	999	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	75.2101	58	999	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.0746	55	999	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	74.9932	64	999	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:53:42,969] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12633/tc_result.tsv
[2023-03-14 14:53:42,969] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:53:42,969] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:53:42,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfef3f9e5-b26e-420e-9865-6832df3e30e8/dqc_reference/checkm_data
[2023-03-14 14:53:42,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:53:42,974] [INFO] Task started: CheckM
[2023-03-14 14:53:42,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12633/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12633/checkm_input OceanDNA-b12633/checkm_result
[2023-03-14 14:54:34,558] [INFO] Task succeeded: CheckM
[2023-03-14 14:54:34,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 14:54:34,561] [INFO] ===== Completeness check finished =====
[2023-03-14 14:54:34,562] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:54:34,562] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12633/markers.fasta)
[2023-03-14 14:54:34,563] [INFO] Task started: Blastn
[2023-03-14 14:54:34,563] [INFO] Running command: blastn -query OceanDNA-b12633/markers.fasta -db /var/lib/cwl/stgfef3f9e5-b26e-420e-9865-6832df3e30e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12633/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:54:35,442] [INFO] Task succeeded: Blastn
[2023-03-14 14:54:35,443] [INFO] Selected 11 target genomes.
[2023-03-14 14:54:35,443] [INFO] Target genome list was writen to OceanDNA-b12633/target_genomes_gtdb.txt
[2023-03-14 14:54:35,456] [INFO] Task started: fastANI
[2023-03-14 14:54:35,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a78878d-c9af-4bbb-9b2a-e89653137c08/OceanDNA-b12633.fa --refList OceanDNA-b12633/target_genomes_gtdb.txt --output OceanDNA-b12633/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:54:46,234] [INFO] Task succeeded: fastANI
[2023-03-14 14:54:46,241] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:54:46,241] [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_905479915.1	s__GCA-002793235 sp905479915	79.4924	437	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401955.1	s__GCA-002793235 sp002401955	79.4147	450	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763795.1	s__GCA-002793235 sp016763795	78.2984	351	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763135.1	s__GCA-002793235 sp016763135	77.8094	263	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479995.1	s__GCA-002793235 sp905479995	77.7384	213	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002402165.1	s__GCA-002793235 sp002402165	77.5293	288	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993035.1	s__Vicingus serpentipes	76.9887	210	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002790175.1	s__GCA-002793235 sp002790175	76.655	152	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	99.29	99.29	0.84	0.84	2	-
GCA_002770955.1	s__BRH-c54 sp002770955	75.8051	101	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	99.41	99.41	0.88	0.88	2	-
GCA_002841035.1	s__BRH-c54 sp002841035	75.5854	65	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:54:46,241] [INFO] GTDB search result was written to OceanDNA-b12633/result_gtdb.tsv
[2023-03-14 14:54:46,241] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:54:46,242] [INFO] DFAST_QC result json was written to OceanDNA-b12633/dqc_result.json
[2023-03-14 14:54:46,242] [INFO] DFAST_QC completed!
[2023-03-14 14:54:46,242] [INFO] Total running time: 0h1m50s