[2023-06-05 00:38:10,027] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:38:10,031] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:38:10,031] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8eb82e3-8e3b-4f4c-b7d9-d72276a4912c/dqc_reference
[2023-06-05 00:38:11,475] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:38:11,477] [INFO] Task started: Prodigal
[2023-06-05 00:38:11,477] [INFO] Running command: gunzip -c /var/lib/cwl/stga27a9f48-61d3-4ef1-a9a7-b1350d61fdaa/GCA_934339005.1_ERR7746285_bin.3_genomic.fna.gz | prodigal -d GCA_934339005.1_ERR7746285_bin.3_genomic.fna/cds.fna -a GCA_934339005.1_ERR7746285_bin.3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:38:18,854] [INFO] Task succeeded: Prodigal
[2023-06-05 00:38:18,854] [INFO] Task started: HMMsearch
[2023-06-05 00:38:18,854] [INFO] Running command: hmmsearch --tblout GCA_934339005.1_ERR7746285_bin.3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8eb82e3-8e3b-4f4c-b7d9-d72276a4912c/dqc_reference/reference_markers.hmm GCA_934339005.1_ERR7746285_bin.3_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:38:19,153] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:38:19,154] [INFO] Found 6/6 markers.
[2023-06-05 00:38:19,183] [INFO] Query marker FASTA was written to GCA_934339005.1_ERR7746285_bin.3_genomic.fna/markers.fasta
[2023-06-05 00:38:19,184] [INFO] Task started: Blastn
[2023-06-05 00:38:19,184] [INFO] Running command: blastn -query GCA_934339005.1_ERR7746285_bin.3_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8eb82e3-8e3b-4f4c-b7d9-d72276a4912c/dqc_reference/reference_markers.fasta -out GCA_934339005.1_ERR7746285_bin.3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:19,859] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:19,864] [INFO] Selected 31 target genomes.
[2023-06-05 00:38:19,865] [INFO] Target genome list was writen to GCA_934339005.1_ERR7746285_bin.3_genomic.fna/target_genomes.txt
[2023-06-05 00:38:19,866] [INFO] Task started: fastANI
[2023-06-05 00:38:19,866] [INFO] Running command: fastANI --query /var/lib/cwl/stga27a9f48-61d3-4ef1-a9a7-b1350d61fdaa/GCA_934339005.1_ERR7746285_bin.3_genomic.fna.gz --refList GCA_934339005.1_ERR7746285_bin.3_genomic.fna/target_genomes.txt --output GCA_934339005.1_ERR7746285_bin.3_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:38:36,435] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:36,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8eb82e3-8e3b-4f4c-b7d9-d72276a4912c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:38:36,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8eb82e3-8e3b-4f4c-b7d9-d72276a4912c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:38:36,455] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:38:36,455] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:38:36,456] [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
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	77.3909	107	954	95	below_threshold
Coprococcus catus	strain=VPIC661	GCA_019734885.1	116085	116085	suspected-type	True	77.3592	107	954	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	76.7906	74	954	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	76.7613	62	954	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	76.7545	62	954	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	76.6302	64	954	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	76.6269	54	954	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	76.6214	53	954	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	76.6113	69	954	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	76.5538	61	954	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	76.5418	58	954	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	76.4426	58	954	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.2977	50	954	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	76.274	58	954	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:38:36,458] [INFO] DFAST Taxonomy check result was written to GCA_934339005.1_ERR7746285_bin.3_genomic.fna/tc_result.tsv
[2023-06-05 00:38:36,459] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:38:36,459] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:38:36,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8eb82e3-8e3b-4f4c-b7d9-d72276a4912c/dqc_reference/checkm_data
[2023-06-05 00:38:36,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:38:36,500] [INFO] Task started: CheckM
[2023-06-05 00:38:36,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934339005.1_ERR7746285_bin.3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934339005.1_ERR7746285_bin.3_genomic.fna/checkm_input GCA_934339005.1_ERR7746285_bin.3_genomic.fna/checkm_result
[2023-06-05 00:39:04,893] [INFO] Task succeeded: CheckM
[2023-06-05 00:39:04,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:39:04,915] [INFO] ===== Completeness check finished =====
[2023-06-05 00:39:04,916] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:39:04,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934339005.1_ERR7746285_bin.3_genomic.fna/markers.fasta)
[2023-06-05 00:39:04,916] [INFO] Task started: Blastn
[2023-06-05 00:39:04,917] [INFO] Running command: blastn -query GCA_934339005.1_ERR7746285_bin.3_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8eb82e3-8e3b-4f4c-b7d9-d72276a4912c/dqc_reference/reference_markers_gtdb.fasta -out GCA_934339005.1_ERR7746285_bin.3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:39:05,948] [INFO] Task succeeded: Blastn
[2023-06-05 00:39:05,953] [INFO] Selected 31 target genomes.
[2023-06-05 00:39:05,954] [INFO] Target genome list was writen to GCA_934339005.1_ERR7746285_bin.3_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:39:06,101] [INFO] Task started: fastANI
[2023-06-05 00:39:06,101] [INFO] Running command: fastANI --query /var/lib/cwl/stga27a9f48-61d3-4ef1-a9a7-b1350d61fdaa/GCA_934339005.1_ERR7746285_bin.3_genomic.fna.gz --refList GCA_934339005.1_ERR7746285_bin.3_genomic.fna/target_genomes_gtdb.txt --output GCA_934339005.1_ERR7746285_bin.3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:39:19,597] [INFO] Task succeeded: fastANI
[2023-06-05 00:39:19,618] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:39:19,619] [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_018785175.1	s__Coprococcus_A sp900548825	77.3747	100	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus_A	95.0	98.21	98.06	0.90	0.89	4	-
GCF_902381825.1	s__Coprococcus_A catus	77.3633	115	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus_A	95.0	98.33	97.35	0.89	0.80	8	-
GCA_905199445.1	s__Catenibacillus sp900553975	77.3589	78	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	99.69	99.69	0.90	0.90	2	-
GCA_009929615.1	s__Frisingicoccus sp009929615	77.0386	81	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.91	99.91	0.88	0.88	2	-
GCA_017391465.1	s__Frisingicoccus sp017391465	76.9242	66	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711005.1	s__Catenibacillus faecigallinarum	76.6032	67	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	99.82	99.82	0.94	0.94	2	-
GCA_018369015.1	s__Catenibacillus sp018369015	76.5919	60	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539145.1	s__Blautia sp900539145	76.5094	53	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.09	98.22	0.85	0.80	3	-
GCF_001404655.1	s__Anaerostipes hadrus_A	76.4995	55	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.11	98.66	0.92	0.88	9	-
GCA_017437065.1	s__RGIG3002 sp017437065	76.4986	58	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057635.1	s__Lachnoclostridium sp015057635	76.4614	50	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547685.1	s__Blautia sp900547685	76.0896	58	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201915.1	s__Blautia sp900555025	75.7842	54	954	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.26	99.26	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-05 00:39:19,621] [INFO] GTDB search result was written to GCA_934339005.1_ERR7746285_bin.3_genomic.fna/result_gtdb.tsv
[2023-06-05 00:39:19,621] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:39:19,625] [INFO] DFAST_QC result json was written to GCA_934339005.1_ERR7746285_bin.3_genomic.fna/dqc_result.json
[2023-06-05 00:39:19,626] [INFO] DFAST_QC completed!
[2023-06-05 00:39:19,626] [INFO] Total running time: 0h1m10s