[2023-06-13 14:45:16,988] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:45:16,990] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:45:16,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg699018d5-f892-4cfb-9efb-31082da76b8a/dqc_reference
[2023-06-13 14:45:18,122] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:45:18,122] [INFO] Task started: Prodigal
[2023-06-13 14:45:18,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b36e71c-b550-4b19-88d4-ebdf77442f01/GCA_947464045.1_RE-27jun17-179_genomic.fna.gz | prodigal -d GCA_947464045.1_RE-27jun17-179_genomic.fna/cds.fna -a GCA_947464045.1_RE-27jun17-179_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:45:22,194] [INFO] Task succeeded: Prodigal
[2023-06-13 14:45:22,195] [INFO] Task started: HMMsearch
[2023-06-13 14:45:22,195] [INFO] Running command: hmmsearch --tblout GCA_947464045.1_RE-27jun17-179_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg699018d5-f892-4cfb-9efb-31082da76b8a/dqc_reference/reference_markers.hmm GCA_947464045.1_RE-27jun17-179_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:45:22,351] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:45:22,352] [INFO] Found 6/6 markers.
[2023-06-13 14:45:22,372] [INFO] Query marker FASTA was written to GCA_947464045.1_RE-27jun17-179_genomic.fna/markers.fasta
[2023-06-13 14:45:22,372] [INFO] Task started: Blastn
[2023-06-13 14:45:22,372] [INFO] Running command: blastn -query GCA_947464045.1_RE-27jun17-179_genomic.fna/markers.fasta -db /var/lib/cwl/stg699018d5-f892-4cfb-9efb-31082da76b8a/dqc_reference/reference_markers.fasta -out GCA_947464045.1_RE-27jun17-179_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:23,009] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:23,012] [INFO] Selected 19 target genomes.
[2023-06-13 14:45:23,013] [INFO] Target genome list was writen to GCA_947464045.1_RE-27jun17-179_genomic.fna/target_genomes.txt
[2023-06-13 14:45:23,013] [INFO] Task started: fastANI
[2023-06-13 14:45:23,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b36e71c-b550-4b19-88d4-ebdf77442f01/GCA_947464045.1_RE-27jun17-179_genomic.fna.gz --refList GCA_947464045.1_RE-27jun17-179_genomic.fna/target_genomes.txt --output GCA_947464045.1_RE-27jun17-179_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:45:38,624] [INFO] Task succeeded: fastANI
[2023-06-13 14:45:38,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg699018d5-f892-4cfb-9efb-31082da76b8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:45:38,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg699018d5-f892-4cfb-9efb-31082da76b8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:45:38,631] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:45:38,631] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:45:38,631] [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
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	77.2854	51	485	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	77.1676	57	485	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	77.1348	64	485	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.9464	56	485	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.7961	59	485	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.5549	61	485	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:45:38,633] [INFO] DFAST Taxonomy check result was written to GCA_947464045.1_RE-27jun17-179_genomic.fna/tc_result.tsv
[2023-06-13 14:45:38,633] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:45:38,633] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:45:38,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg699018d5-f892-4cfb-9efb-31082da76b8a/dqc_reference/checkm_data
[2023-06-13 14:45:38,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:45:38,655] [INFO] Task started: CheckM
[2023-06-13 14:45:38,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947464045.1_RE-27jun17-179_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947464045.1_RE-27jun17-179_genomic.fna/checkm_input GCA_947464045.1_RE-27jun17-179_genomic.fna/checkm_result
[2023-06-13 14:45:56,283] [INFO] Task succeeded: CheckM
[2023-06-13 14:45:56,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.52%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 14:45:56,308] [INFO] ===== Completeness check finished =====
[2023-06-13 14:45:56,308] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:45:56,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947464045.1_RE-27jun17-179_genomic.fna/markers.fasta)
[2023-06-13 14:45:56,309] [INFO] Task started: Blastn
[2023-06-13 14:45:56,310] [INFO] Running command: blastn -query GCA_947464045.1_RE-27jun17-179_genomic.fna/markers.fasta -db /var/lib/cwl/stg699018d5-f892-4cfb-9efb-31082da76b8a/dqc_reference/reference_markers_gtdb.fasta -out GCA_947464045.1_RE-27jun17-179_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:57,347] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:57,350] [INFO] Selected 13 target genomes.
[2023-06-13 14:45:57,350] [INFO] Target genome list was writen to GCA_947464045.1_RE-27jun17-179_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:45:57,351] [INFO] Task started: fastANI
[2023-06-13 14:45:57,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b36e71c-b550-4b19-88d4-ebdf77442f01/GCA_947464045.1_RE-27jun17-179_genomic.fna.gz --refList GCA_947464045.1_RE-27jun17-179_genomic.fna/target_genomes_gtdb.txt --output GCA_947464045.1_RE-27jun17-179_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:46:03,140] [INFO] Task succeeded: fastANI
[2023-06-13 14:46:03,148] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:46:03,148] [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_903910215.1	s__UBA964 sp903910215	98.5617	378	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.86	98.86	0.82	0.82	2	conclusive
GCA_018970145.1	s__UBA964 sp018970145	85.4488	445	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885195.1	s__UBA964 sp903885195	79.2388	178	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.55	99.16	0.90	0.86	6	-
GCA_018883185.1	s__UBA964 sp018883185	78.5226	153	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853555.1	s__UBA964 sp017853555	78.4683	154	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010031985.1	s__UBA964 sp010031985	78.2348	132	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.93	98.76	0.80	0.76	12	-
GCA_016874175.1	s__UBA964 sp016874175	78.1534	160	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874235.1	s__UBA964 sp016874235	78.1428	130	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	95.25	95.25	0.78	0.78	2	-
GCA_010027845.1	s__UBA964 sp010027845	77.9628	134	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938365.1	s__UBA964 sp903938365	77.9056	124	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.27	99.13	0.88	0.87	4	-
GCA_016874555.1	s__UBA964 sp016874555	77.7397	109	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853175.1	s__UBA964 sp017853175	77.7015	129	485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:46:03,150] [INFO] GTDB search result was written to GCA_947464045.1_RE-27jun17-179_genomic.fna/result_gtdb.tsv
[2023-06-13 14:46:03,150] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:46:03,153] [INFO] DFAST_QC result json was written to GCA_947464045.1_RE-27jun17-179_genomic.fna/dqc_result.json
[2023-06-13 14:46:03,153] [INFO] DFAST_QC completed!
[2023-06-13 14:46:03,153] [INFO] Total running time: 0h0m46s