[2023-03-16 20:18:59,111] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:18:59,112] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:18:59,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg932b36ac-ab60-44e5-9cb2-c947fa13d9b3/dqc_reference
[2023-03-16 20:19:00,199] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:19:00,200] [INFO] Task started: Prodigal
[2023-03-16 20:19:00,201] [INFO] Running command: cat /var/lib/cwl/stg3c3b9be5-8272-4270-96b5-dd6a8929225a/OceanDNA-b3599.fa | prodigal -d OceanDNA-b3599/cds.fna -a OceanDNA-b3599/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:19:24,441] [INFO] Task succeeded: Prodigal
[2023-03-16 20:19:24,442] [INFO] Task started: HMMsearch
[2023-03-16 20:19:24,442] [INFO] Running command: hmmsearch --tblout OceanDNA-b3599/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg932b36ac-ab60-44e5-9cb2-c947fa13d9b3/dqc_reference/reference_markers.hmm OceanDNA-b3599/protein.faa > /dev/null
[2023-03-16 20:19:24,656] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:19:24,656] [INFO] Found 6/6 markers.
[2023-03-16 20:19:24,676] [INFO] Query marker FASTA was written to OceanDNA-b3599/markers.fasta
[2023-03-16 20:19:24,677] [INFO] Task started: Blastn
[2023-03-16 20:19:24,677] [INFO] Running command: blastn -query OceanDNA-b3599/markers.fasta -db /var/lib/cwl/stg932b36ac-ab60-44e5-9cb2-c947fa13d9b3/dqc_reference/reference_markers.fasta -out OceanDNA-b3599/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:19:25,250] [INFO] Task succeeded: Blastn
[2023-03-16 20:19:25,250] [INFO] Selected 22 target genomes.
[2023-03-16 20:19:25,251] [INFO] Target genome list was writen to OceanDNA-b3599/target_genomes.txt
[2023-03-16 20:19:25,264] [INFO] Task started: fastANI
[2023-03-16 20:19:25,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c3b9be5-8272-4270-96b5-dd6a8929225a/OceanDNA-b3599.fa --refList OceanDNA-b3599/target_genomes.txt --output OceanDNA-b3599/fastani_result.tsv --threads 1
[2023-03-16 20:19:42,352] [INFO] Task succeeded: fastANI
[2023-03-16 20:19:42,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg932b36ac-ab60-44e5-9cb2-c947fa13d9b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:19:42,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg932b36ac-ab60-44e5-9cb2-c947fa13d9b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:19:42,367] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:19:42,367] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:19:42,367] [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
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	79.0547	454	1080	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	77.9098	145	1080	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	77.3091	165	1080	95	below_threshold
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	77.3026	105	1080	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.6721	67	1080	95	below_threshold
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	76.6611	62	1080	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	76.6183	83	1080	95	below_threshold
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	76.6098	120	1080	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.4814	60	1080	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	76.2374	56	1080	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	76.1899	96	1080	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:19:42,367] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3599/tc_result.tsv
[2023-03-16 20:19:42,367] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:19:42,367] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:19:42,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg932b36ac-ab60-44e5-9cb2-c947fa13d9b3/dqc_reference/checkm_data
[2023-03-16 20:19:42,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:19:42,373] [INFO] Task started: CheckM
[2023-03-16 20:19:42,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3599/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3599/checkm_input OceanDNA-b3599/checkm_result
[2023-03-16 20:20:59,157] [INFO] Task succeeded: CheckM
[2023-03-16 20:20:59,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:20:59,166] [INFO] ===== Completeness check finished =====
[2023-03-16 20:20:59,166] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:20:59,166] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3599/markers.fasta)
[2023-03-16 20:20:59,168] [INFO] Task started: Blastn
[2023-03-16 20:20:59,168] [INFO] Running command: blastn -query OceanDNA-b3599/markers.fasta -db /var/lib/cwl/stg932b36ac-ab60-44e5-9cb2-c947fa13d9b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3599/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:21:00,553] [INFO] Task succeeded: Blastn
[2023-03-16 20:21:00,554] [INFO] Selected 11 target genomes.
[2023-03-16 20:21:00,554] [INFO] Target genome list was writen to OceanDNA-b3599/target_genomes_gtdb.txt
[2023-03-16 20:21:00,569] [INFO] Task started: fastANI
[2023-03-16 20:21:00,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c3b9be5-8272-4270-96b5-dd6a8929225a/OceanDNA-b3599.fa --refList OceanDNA-b3599/target_genomes_gtdb.txt --output OceanDNA-b3599/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:21:14,351] [INFO] Task succeeded: fastANI
[2023-03-16 20:21:14,358] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:21:14,359] [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_013391385.1	s__Sediminibacterium sp013391385	98.2702	989	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012270485.1	s__Sediminibacterium sp012270485	92.6089	897	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741945.1	s__Sediminibacterium sp016741945	87.625	546	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003526435.1	s__Sediminibacterium sp003526435	79.0861	346	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361915.1	s__Sediminibacterium goheungense	79.0738	454	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996675.1	s__Sediminibacterium sp009996675	77.6696	265	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183765.1	s__Sediminibacterium sp016183765	77.3415	175	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913355.1	s__Sediminibacterium sp903913355	77.0976	143	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297075.1	s__Sediminibacterium sp004297075	76.7373	134	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.05	98.05	0.89	0.89	2	-
GCA_004028765.1	s__Sediminibacterium sp004028765	76.594	172	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337145.1	s__UBA1930 sp002337145	76.4715	69	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA1930	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-16 20:21:14,359] [INFO] GTDB search result was written to OceanDNA-b3599/result_gtdb.tsv
[2023-03-16 20:21:14,359] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:21:14,361] [INFO] DFAST_QC result json was written to OceanDNA-b3599/dqc_result.json
[2023-03-16 20:21:14,361] [INFO] DFAST_QC completed!
[2023-03-16 20:21:14,361] [INFO] Total running time: 0h2m15s