[2023-06-08 03:31:18,044] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:31:18,046] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:31:18,046] [INFO] DQC Reference Directory: /var/lib/cwl/stgf33909a2-8e12-4621-959d-9ac28e14987f/dqc_reference
[2023-06-08 03:31:19,256] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:31:19,257] [INFO] Task started: Prodigal
[2023-06-08 03:31:19,257] [INFO] Running command: gunzip -c /var/lib/cwl/stg416ef35b-14df-477b-bf00-76776a7caf5a/GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:31:27,513] [INFO] Task succeeded: Prodigal
[2023-06-08 03:31:27,514] [INFO] Task started: HMMsearch
[2023-06-08 03:31:27,514] [INFO] Running command: hmmsearch --tblout GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf33909a2-8e12-4621-959d-9ac28e14987f/dqc_reference/reference_markers.hmm GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:31:27,791] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:31:27,792] [INFO] Found 6/6 markers.
[2023-06-08 03:31:27,823] [INFO] Query marker FASTA was written to GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 03:31:27,824] [INFO] Task started: Blastn
[2023-06-08 03:31:27,824] [INFO] Running command: blastn -query GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf33909a2-8e12-4621-959d-9ac28e14987f/dqc_reference/reference_markers.fasta -out GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:31:28,449] [INFO] Task succeeded: Blastn
[2023-06-08 03:31:28,454] [INFO] Selected 23 target genomes.
[2023-06-08 03:31:28,454] [INFO] Target genome list was writen to GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 03:31:28,460] [INFO] Task started: fastANI
[2023-06-08 03:31:28,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg416ef35b-14df-477b-bf00-76776a7caf5a/GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:31:43,699] [INFO] Task succeeded: fastANI
[2023-06-08 03:31:43,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf33909a2-8e12-4621-959d-9ac28e14987f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:31:43,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf33909a2-8e12-4621-959d-9ac28e14987f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:31:43,717] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:31:43,717] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 03:31:43,717] [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
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.6182	116	1135	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.5723	115	1135	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.5602	118	1135	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.5512	110	1135	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.4151	119	1135	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	76.4104	73	1135	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.4051	101	1135	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.3831	107	1135	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.2601	103	1135	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.1997	159	1135	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.1781	158	1135	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.0232	70	1135	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.0029	73	1135	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 03:31:43,719] [INFO] DFAST Taxonomy check result was written to GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 03:31:43,719] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:31:43,719] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:31:43,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf33909a2-8e12-4621-959d-9ac28e14987f/dqc_reference/checkm_data
[2023-06-08 03:31:43,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:31:43,756] [INFO] Task started: CheckM
[2023-06-08 03:31:43,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 03:32:13,378] [INFO] Task succeeded: CheckM
[2023-06-08 03:32:13,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:32:13,402] [INFO] ===== Completeness check finished =====
[2023-06-08 03:32:13,402] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:32:13,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 03:32:13,403] [INFO] Task started: Blastn
[2023-06-08 03:32:13,403] [INFO] Running command: blastn -query GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf33909a2-8e12-4621-959d-9ac28e14987f/dqc_reference/reference_markers_gtdb.fasta -out GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:32:14,469] [INFO] Task succeeded: Blastn
[2023-06-08 03:32:14,475] [INFO] Selected 22 target genomes.
[2023-06-08 03:32:14,475] [INFO] Target genome list was writen to GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:32:14,483] [INFO] Task started: fastANI
[2023-06-08 03:32:14,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg416ef35b-14df-477b-bf00-76776a7caf5a/GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:32:29,138] [INFO] Task succeeded: fastANI
[2023-06-08 03:32:29,163] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:32:29,163] [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_910575565.1	s__Caccovicinus sp910575565	99.2482	1082	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.12	99.12	0.93	0.93	2	conclusive
GCA_910589195.1	s__Caccovicinus sp910589195	78.6433	393	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774615.1	s__Caccovicinus sp009774615	78.0816	287	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.13	99.13	0.87	0.87	2	-
GCA_910585635.1	s__Caccovicinus sp910585635	77.8438	289	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889125.1	s__Caccovicinus sp017889125	77.5934	246	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588895.1	s__Caccovicinus sp910588895	77.4226	249	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715905.1	s__Caccovicinus merdipullorum	77.4154	214	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCA_003611875.1	s__Ventrimonas sp003611875	77.3385	150	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.50	99.24	0.91	0.86	4	-
GCA_018713255.1	s__Caccovicinus excrementipullorum	77.3059	195	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.99	99.99	0.96	0.96	2	-
GCA_910586255.1	s__Ventrimonas sp910586255	76.7721	161	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018380885.1	s__Enterocloster sp900555905	76.6347	148	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
GCA_019114465.1	s__Lachnoclostridium_A avicola	76.5697	83	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.23	98.89	0.92	0.90	3	-
GCF_002160755.1	s__Lachnoclostridium_A sp002160755	76.5433	134	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.32	98.32	0.92	0.92	2	-
GCA_002160535.1	s__Clostridium_Q saccharolyticum_A	76.5387	81	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.86	98.46	0.90	0.84	10	-
GCA_904395885.1	s__UMGS1370 sp904395885	76.4846	79	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1370	95.0	99.37	99.37	0.90	0.90	2	-
GCA_018223415.1	s__Copromonas sp900541255	76.4422	74	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	99.81	99.68	0.96	0.93	4	-
GCA_001304875.1	s__Ventrisoma faecale	76.4164	89	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrisoma	95.0	98.23	97.74	0.91	0.86	4	-
GCA_905215775.1	s__Copromonas sp905215775	76.3577	82	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003434055.1	s__Enterocloster aldenensis	76.2878	141	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.16	97.51	0.89	0.78	13	-
GCA_019118585.1	s__Enterocloster faecavium	76.0855	97	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.87	99.87	0.86	0.86	2	-
GCF_900155545.1	s__Lacrimispora sp900155545	76.0748	84	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119775.1	s__Lachnoclostridium_A pullistercoris	75.9549	92	1135	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.96	99.96	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-08 03:32:29,165] [INFO] GTDB search result was written to GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 03:32:29,165] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:32:29,169] [INFO] DFAST_QC result json was written to GCA_947003205.1_SRR19715300_bin.8_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 03:32:29,169] [INFO] DFAST_QC completed!
[2023-06-08 03:32:29,169] [INFO] Total running time: 0h1m11s