[2023-06-05 19:01:13,927] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:01:13,929] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:01:13,930] [INFO] DQC Reference Directory: /var/lib/cwl/stgab40dd07-349e-48f1-86b6-2e74146e7313/dqc_reference
[2023-06-05 19:01:15,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:01:15,116] [INFO] Task started: Prodigal
[2023-06-05 19:01:15,117] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7462a1b-1ed9-46ef-805c-11e68aec66d3/GCA_934307705.1_ERR7738592_bin.36_genomic.fna.gz | prodigal -d GCA_934307705.1_ERR7738592_bin.36_genomic.fna/cds.fna -a GCA_934307705.1_ERR7738592_bin.36_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:01:22,673] [INFO] Task succeeded: Prodigal
[2023-06-05 19:01:22,674] [INFO] Task started: HMMsearch
[2023-06-05 19:01:22,674] [INFO] Running command: hmmsearch --tblout GCA_934307705.1_ERR7738592_bin.36_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab40dd07-349e-48f1-86b6-2e74146e7313/dqc_reference/reference_markers.hmm GCA_934307705.1_ERR7738592_bin.36_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:01:22,932] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:01:22,934] [INFO] Found 6/6 markers.
[2023-06-05 19:01:22,966] [INFO] Query marker FASTA was written to GCA_934307705.1_ERR7738592_bin.36_genomic.fna/markers.fasta
[2023-06-05 19:01:22,967] [INFO] Task started: Blastn
[2023-06-05 19:01:22,967] [INFO] Running command: blastn -query GCA_934307705.1_ERR7738592_bin.36_genomic.fna/markers.fasta -db /var/lib/cwl/stgab40dd07-349e-48f1-86b6-2e74146e7313/dqc_reference/reference_markers.fasta -out GCA_934307705.1_ERR7738592_bin.36_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:01:23,622] [INFO] Task succeeded: Blastn
[2023-06-05 19:01:23,628] [INFO] Selected 20 target genomes.
[2023-06-05 19:01:23,628] [INFO] Target genome list was writen to GCA_934307705.1_ERR7738592_bin.36_genomic.fna/target_genomes.txt
[2023-06-05 19:01:23,630] [INFO] Task started: fastANI
[2023-06-05 19:01:23,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7462a1b-1ed9-46ef-805c-11e68aec66d3/GCA_934307705.1_ERR7738592_bin.36_genomic.fna.gz --refList GCA_934307705.1_ERR7738592_bin.36_genomic.fna/target_genomes.txt --output GCA_934307705.1_ERR7738592_bin.36_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:01:34,280] [INFO] Task succeeded: fastANI
[2023-06-05 19:01:34,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab40dd07-349e-48f1-86b6-2e74146e7313/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:01:34,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab40dd07-349e-48f1-86b6-2e74146e7313/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:01:34,300] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 19:01:34,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 19:01:34,301] [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 inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	96.5205	799	986	95	conclusive
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	79.2039	331	986	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	79.1896	317	986	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	79.1175	319	986	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.3821	192	986	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.1423	91	986	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	78.0152	213	986	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	77.6157	83	986	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	77.6083	86	986	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	77.5169	64	986	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	77.2245	85	986	95	below_threshold
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	76.8243	75	986	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.6589	89	986	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.5562	58	986	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	76.5121	59	986	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.4771	53	986	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:01:34,303] [INFO] DFAST Taxonomy check result was written to GCA_934307705.1_ERR7738592_bin.36_genomic.fna/tc_result.tsv
[2023-06-05 19:01:34,304] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:01:34,304] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:01:34,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab40dd07-349e-48f1-86b6-2e74146e7313/dqc_reference/checkm_data
[2023-06-05 19:01:34,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:01:34,338] [INFO] Task started: CheckM
[2023-06-05 19:01:34,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934307705.1_ERR7738592_bin.36_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934307705.1_ERR7738592_bin.36_genomic.fna/checkm_input GCA_934307705.1_ERR7738592_bin.36_genomic.fna/checkm_result
[2023-06-05 19:02:03,264] [INFO] Task succeeded: CheckM
[2023-06-05 19:02:03,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 19:02:03,288] [INFO] ===== Completeness check finished =====
[2023-06-05 19:02:03,288] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:02:03,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934307705.1_ERR7738592_bin.36_genomic.fna/markers.fasta)
[2023-06-05 19:02:03,289] [INFO] Task started: Blastn
[2023-06-05 19:02:03,289] [INFO] Running command: blastn -query GCA_934307705.1_ERR7738592_bin.36_genomic.fna/markers.fasta -db /var/lib/cwl/stgab40dd07-349e-48f1-86b6-2e74146e7313/dqc_reference/reference_markers_gtdb.fasta -out GCA_934307705.1_ERR7738592_bin.36_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:04,325] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:04,330] [INFO] Selected 14 target genomes.
[2023-06-05 19:02:04,330] [INFO] Target genome list was writen to GCA_934307705.1_ERR7738592_bin.36_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:02:04,333] [INFO] Task started: fastANI
[2023-06-05 19:02:04,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7462a1b-1ed9-46ef-805c-11e68aec66d3/GCA_934307705.1_ERR7738592_bin.36_genomic.fna.gz --refList GCA_934307705.1_ERR7738592_bin.36_genomic.fna/target_genomes_gtdb.txt --output GCA_934307705.1_ERR7738592_bin.36_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:02:13,064] [INFO] Task succeeded: fastANI
[2023-06-05 19:02:13,082] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:02:13,083] [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
GCF_000174195.1	s__Roseburia inulinivorans	96.5205	799	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	conclusive
GCA_900542495.1	s__Roseburia sp900542495	90.304	734	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.47	97.09	0.82	0.76	4	-
GCA_900756925.1	s__Roseburia sp900756925	80.3196	211	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.83	98.83	0.90	0.90	2	-
GCA_003483745.1	s__Roseburia sp003483745	79.253	301	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCF_003470905.1	s__Roseburia sp003470905	79.1396	322	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCF_900537995.1	s__Roseburia intestinalis	79.1215	320	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCF_001940165.1	s__Roseburia sp001940165	78.8209	256	986	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_900550935.1	s__Roseburia sp900550935	78.5312	233	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCA_902363825.1	s__CAG-45 sp000438375	78.0237	143	986	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	-
GCF_000225345.1	s__Roseburia hominis	77.9836	211	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCA_017547315.1	s__Roseburia sp017547315	77.5993	82	986	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_900116395.1	s__XBD2001 sp900116395	76.782	54	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__XBD2001	95.0	96.26	95.68	0.91	0.86	9	-
GCA_015057085.1	s__Agathobacter sp015057085	76.6172	75	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 19:02:13,085] [INFO] GTDB search result was written to GCA_934307705.1_ERR7738592_bin.36_genomic.fna/result_gtdb.tsv
[2023-06-05 19:02:13,086] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:02:13,090] [INFO] DFAST_QC result json was written to GCA_934307705.1_ERR7738592_bin.36_genomic.fna/dqc_result.json
[2023-06-05 19:02:13,090] [INFO] DFAST_QC completed!
[2023-06-05 19:02:13,090] [INFO] Total running time: 0h0m59s