[2023-06-16 19:17:14,188] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:17:14,190] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:17:14,191] [INFO] DQC Reference Directory: /var/lib/cwl/stgff6e4197-2aa0-40eb-b65d-7712a4f9a341/dqc_reference
[2023-06-16 19:17:15,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:17:15,348] [INFO] Task started: Prodigal
[2023-06-16 19:17:15,348] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ce68ec5-6e41-4bc0-bf10-97566c3caab0/GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna.gz | prodigal -d GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/cds.fna -a GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:17:21,131] [INFO] Task succeeded: Prodigal
[2023-06-16 19:17:21,132] [INFO] Task started: HMMsearch
[2023-06-16 19:17:21,132] [INFO] Running command: hmmsearch --tblout GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff6e4197-2aa0-40eb-b65d-7712a4f9a341/dqc_reference/reference_markers.hmm GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:17:21,296] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:17:21,298] [INFO] Found 6/6 markers.
[2023-06-16 19:17:21,317] [INFO] Query marker FASTA was written to GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/markers.fasta
[2023-06-16 19:17:21,317] [INFO] Task started: Blastn
[2023-06-16 19:17:21,317] [INFO] Running command: blastn -query GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/markers.fasta -db /var/lib/cwl/stgff6e4197-2aa0-40eb-b65d-7712a4f9a341/dqc_reference/reference_markers.fasta -out GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:17:22,004] [INFO] Task succeeded: Blastn
[2023-06-16 19:17:22,008] [INFO] Selected 13 target genomes.
[2023-06-16 19:17:22,009] [INFO] Target genome list was writen to GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/target_genomes.txt
[2023-06-16 19:17:22,009] [INFO] Task started: fastANI
[2023-06-16 19:17:22,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce68ec5-6e41-4bc0-bf10-97566c3caab0/GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna.gz --refList GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/target_genomes.txt --output GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:17:27,286] [INFO] Task succeeded: fastANI
[2023-06-16 19:17:27,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff6e4197-2aa0-40eb-b65d-7712a4f9a341/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:17:27,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff6e4197-2aa0-40eb-b65d-7712a4f9a341/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:17:27,297] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:17:27,297] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:17:27,297] [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
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	92.2287	524	619	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	92.2192	521	619	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	92.1537	529	619	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.0967	231	619	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.9516	206	619	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.9115	212	619	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.8656	242	619	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.844	241	619	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.3442	222	619	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.2861	224	619	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.176	195	619	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:17:27,299] [INFO] DFAST Taxonomy check result was written to GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/tc_result.tsv
[2023-06-16 19:17:27,300] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:17:27,300] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:17:27,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff6e4197-2aa0-40eb-b65d-7712a4f9a341/dqc_reference/checkm_data
[2023-06-16 19:17:27,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:17:27,324] [INFO] Task started: CheckM
[2023-06-16 19:17:27,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/checkm_input GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/checkm_result
[2023-06-16 19:17:49,454] [INFO] Task succeeded: CheckM
[2023-06-16 19:17:49,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:17:49,472] [INFO] ===== Completeness check finished =====
[2023-06-16 19:17:49,473] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:17:49,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/markers.fasta)
[2023-06-16 19:17:49,473] [INFO] Task started: Blastn
[2023-06-16 19:17:49,473] [INFO] Running command: blastn -query GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/markers.fasta -db /var/lib/cwl/stgff6e4197-2aa0-40eb-b65d-7712a4f9a341/dqc_reference/reference_markers_gtdb.fasta -out GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:17:50,751] [INFO] Task succeeded: Blastn
[2023-06-16 19:17:50,756] [INFO] Selected 28 target genomes.
[2023-06-16 19:17:50,756] [INFO] Target genome list was writen to GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:17:50,774] [INFO] Task started: fastANI
[2023-06-16 19:17:50,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce68ec5-6e41-4bc0-bf10-97566c3caab0/GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna.gz --refList GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/target_genomes_gtdb.txt --output GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:18:04,130] [INFO] Task succeeded: fastANI
[2023-06-16 19:18:04,153] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:18:04,154] [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_900549275.1	s__Collinsella sp900549275	95.7099	338	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.23	96.21	0.86	0.86	3	conclusive
GCA_900548935.1	s__Collinsella sp900548935	94.4056	412	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900758375.1	s__Collinsella sp900758375	94.2632	479	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.06	0.83	0.78	8	-
GCA_900549085.1	s__Collinsella sp900549085	94.2063	515	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.95	99.95	0.97	0.97	2	-
GCA_900549555.1	s__Collinsella sp900549555	94.1629	468	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.46	95.44	0.81	0.77	3	-
GCA_905215815.1	s__Collinsella sp905215815	94.1067	452	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.63	95.53	0.85	0.84	3	-
GCA_900541475.1	s__Collinsella sp900541475	94.0886	490	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.73	95.01	0.89	0.85	4	-
GCA_900541195.1	s__Collinsella sp900541195	93.9322	511	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541695.1	s__Collinsella sp900541695	93.8939	535	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.64	95.64	0.91	0.91	2	-
GCF_003469185.1	s__Collinsella sp003469185	93.6818	541	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.87	95.38	0.90	0.84	5	-
GCA_905215225.1	s__Collinsella sp905215225	93.5566	354	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554585.1	s__Collinsella sp900554585	93.4794	316	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551625.1	s__Collinsella sp900551625	93.4724	365	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216075.1	s__Collinsella sp905216075	93.3712	398	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550595.1	s__Collinsella sp900550595	93.3522	323	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541045.1	s__Collinsella sp900541045	93.2406	508	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215205.1	s__Collinsella sp905215205	93.1793	351	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015555045.1	s__Collinsella aerofaciens_W	92.8702	514	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547345.1	s__Collinsella sp900547345	92.6009	456	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0188	95.15	95.15	0.87	0.87	2	-
GCA_900752015.1	s__Collinsella sp900752015	92.5613	480	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1642	99.95	99.95	0.93	0.93	2	-
GCA_900551305.1	s__Collinsella sp900551305	92.5443	342	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0792	96.10	95.39	0.89	0.68	9	-
GCA_900544385.1	s__Collinsella sp900544385	92.4454	447	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1115	95.39	95.39	0.85	0.85	2	-
GCF_019041915.1	s__Collinsella sp019041915	92.427	533	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.145	96.63	95.48	0.93	0.87	6	-
GCA_018382125.1	s__Collinsella sp018382125	92.2896	502	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1759	N/A	N/A	N/A	N/A	1	-
GCF_009876115.1	s__Collinsella aerofaciens_N	92.158	525	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.84	99.84	0.98	0.98	2	-
GCA_900554905.1	s__Collinsella sp900554905	92.1484	313	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0183	N/A	N/A	N/A	N/A	1	-
GCA_905208345.1	s__Collinsella sp905208345	92.1357	429	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900544205.1	s__Collinsella sp900544205	92.0488	453	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-16 19:18:04,156] [INFO] GTDB search result was written to GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/result_gtdb.tsv
[2023-06-16 19:18:04,157] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:18:04,162] [INFO] DFAST_QC result json was written to GCA_905209795.1_ERR260257-mag-bin.38_genomic.fna/dqc_result.json
[2023-06-16 19:18:04,162] [INFO] DFAST_QC completed!
[2023-06-16 19:18:04,162] [INFO] Total running time: 0h0m50s