[2023-06-04 17:31:03,308] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:31:03,310] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:31:03,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg41aec09f-0ed4-466f-a3aa-aba5b7b0d0cd/dqc_reference
[2023-06-04 17:31:05,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:31:05,945] [INFO] Task started: Prodigal
[2023-06-04 17:31:05,946] [INFO] Running command: gunzip -c /var/lib/cwl/stga015c133-990a-4db6-8f76-423581a38b85/GCA_934352245.1_ERR7738546_bin.202_genomic.fna.gz | prodigal -d GCA_934352245.1_ERR7738546_bin.202_genomic.fna/cds.fna -a GCA_934352245.1_ERR7738546_bin.202_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:31:12,274] [INFO] Task succeeded: Prodigal
[2023-06-04 17:31:12,275] [INFO] Task started: HMMsearch
[2023-06-04 17:31:12,275] [INFO] Running command: hmmsearch --tblout GCA_934352245.1_ERR7738546_bin.202_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41aec09f-0ed4-466f-a3aa-aba5b7b0d0cd/dqc_reference/reference_markers.hmm GCA_934352245.1_ERR7738546_bin.202_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:31:12,519] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:31:12,521] [INFO] Found 6/6 markers.
[2023-06-04 17:31:12,547] [INFO] Query marker FASTA was written to GCA_934352245.1_ERR7738546_bin.202_genomic.fna/markers.fasta
[2023-06-04 17:31:12,548] [INFO] Task started: Blastn
[2023-06-04 17:31:12,548] [INFO] Running command: blastn -query GCA_934352245.1_ERR7738546_bin.202_genomic.fna/markers.fasta -db /var/lib/cwl/stg41aec09f-0ed4-466f-a3aa-aba5b7b0d0cd/dqc_reference/reference_markers.fasta -out GCA_934352245.1_ERR7738546_bin.202_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:31:13,189] [INFO] Task succeeded: Blastn
[2023-06-04 17:31:13,195] [INFO] Selected 30 target genomes.
[2023-06-04 17:31:13,195] [INFO] Target genome list was writen to GCA_934352245.1_ERR7738546_bin.202_genomic.fna/target_genomes.txt
[2023-06-04 17:31:13,328] [INFO] Task started: fastANI
[2023-06-04 17:31:13,328] [INFO] Running command: fastANI --query /var/lib/cwl/stga015c133-990a-4db6-8f76-423581a38b85/GCA_934352245.1_ERR7738546_bin.202_genomic.fna.gz --refList GCA_934352245.1_ERR7738546_bin.202_genomic.fna/target_genomes.txt --output GCA_934352245.1_ERR7738546_bin.202_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:31:27,695] [INFO] Task succeeded: fastANI
[2023-06-04 17:31:27,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41aec09f-0ed4-466f-a3aa-aba5b7b0d0cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:31:27,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41aec09f-0ed4-466f-a3aa-aba5b7b0d0cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:31:27,709] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:31:27,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:31:27,710] [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
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	78.6103	147	867	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.4034	121	867	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	78.0966	66	867	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.9897	126	867	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.9529	81	867	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.5971	110	867	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.5773	112	867	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	76.7978	58	867	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	76.7722	50	867	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:31:27,712] [INFO] DFAST Taxonomy check result was written to GCA_934352245.1_ERR7738546_bin.202_genomic.fna/tc_result.tsv
[2023-06-04 17:31:27,712] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:31:27,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:31:27,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41aec09f-0ed4-466f-a3aa-aba5b7b0d0cd/dqc_reference/checkm_data
[2023-06-04 17:31:27,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:31:27,746] [INFO] Task started: CheckM
[2023-06-04 17:31:27,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934352245.1_ERR7738546_bin.202_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934352245.1_ERR7738546_bin.202_genomic.fna/checkm_input GCA_934352245.1_ERR7738546_bin.202_genomic.fna/checkm_result
[2023-06-04 17:31:53,216] [INFO] Task succeeded: CheckM
[2023-06-04 17:31:53,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-04 17:31:53,247] [INFO] ===== Completeness check finished =====
[2023-06-04 17:31:53,248] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:31:53,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934352245.1_ERR7738546_bin.202_genomic.fna/markers.fasta)
[2023-06-04 17:31:53,248] [INFO] Task started: Blastn
[2023-06-04 17:31:53,248] [INFO] Running command: blastn -query GCA_934352245.1_ERR7738546_bin.202_genomic.fna/markers.fasta -db /var/lib/cwl/stg41aec09f-0ed4-466f-a3aa-aba5b7b0d0cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_934352245.1_ERR7738546_bin.202_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:31:54,277] [INFO] Task succeeded: Blastn
[2023-06-04 17:31:54,282] [INFO] Selected 15 target genomes.
[2023-06-04 17:31:54,282] [INFO] Target genome list was writen to GCA_934352245.1_ERR7738546_bin.202_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:31:54,550] [INFO] Task started: fastANI
[2023-06-04 17:31:54,550] [INFO] Running command: fastANI --query /var/lib/cwl/stga015c133-990a-4db6-8f76-423581a38b85/GCA_934352245.1_ERR7738546_bin.202_genomic.fna.gz --refList GCA_934352245.1_ERR7738546_bin.202_genomic.fna/target_genomes_gtdb.txt --output GCA_934352245.1_ERR7738546_bin.202_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:32:02,238] [INFO] Task succeeded: fastANI
[2023-06-04 17:32:02,260] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:32:02,261] [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_000020605.1	s__Agathobacter rectalis	97.8242	752	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.37	96.06	0.82	0.65	151	conclusive
GCA_900546625.1	s__Agathobacter sp900546625	94.547	710	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	96.96	96.96	0.86	0.86	2	-
GCA_900317585.1	s__Agathobacter sp900317585	94.5344	618	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.18	95.52	0.87	0.83	5	-
GCA_905209075.1	s__Agathobacter sp905209075	81.2597	303	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.22	97.67	0.80	0.73	5	-
GCA_900549895.1	s__Agathobacter sp900549895	78.8454	97	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552085.1	s__Agathobacter sp900552085	78.5939	104	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_900548765.1	s__Agathobacter sp900548765	78.5839	166	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	97.03	0.78	0.78	2	-
GCA_900543445.1	s__Agathobacter sp900543445	77.6964	124	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
GCA_017937095.1	s__Roseburia sp017937095	77.5617	59	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483745.1	s__Roseburia sp003483745	77.5565	91	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_902363825.1	s__CAG-45 sp000438375	77.2228	68	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	98.60	98.28	0.92	0.87	6	-
GCA_910587655.1	s__Agathobacter sp910587655	77.1048	68	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057035.1	s__Agathobacter sp015057035	76.9898	67	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:32:02,263] [INFO] GTDB search result was written to GCA_934352245.1_ERR7738546_bin.202_genomic.fna/result_gtdb.tsv
[2023-06-04 17:32:02,264] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:32:02,269] [INFO] DFAST_QC result json was written to GCA_934352245.1_ERR7738546_bin.202_genomic.fna/dqc_result.json
[2023-06-04 17:32:02,269] [INFO] DFAST_QC completed!
[2023-06-04 17:32:02,270] [INFO] Total running time: 0h0m59s