[2024-01-24 12:40:36,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:36,150] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:36,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d235c93-b153-47b8-b7fc-4a23b198302c/dqc_reference
[2024-01-24 12:40:37,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:37,381] [INFO] Task started: Prodigal
[2024-01-24 12:40:37,382] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fe10c8a-04ce-4989-b8c5-b229d34a5531/GCF_009696375.1_ASM969637v1_genomic.fna.gz | prodigal -d GCF_009696375.1_ASM969637v1_genomic.fna/cds.fna -a GCF_009696375.1_ASM969637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:47,503] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:47,504] [INFO] Task started: HMMsearch
[2024-01-24 12:40:47,504] [INFO] Running command: hmmsearch --tblout GCF_009696375.1_ASM969637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d235c93-b153-47b8-b7fc-4a23b198302c/dqc_reference/reference_markers.hmm GCF_009696375.1_ASM969637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:47,766] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:47,768] [INFO] Found 6/6 markers.
[2024-01-24 12:40:47,804] [INFO] Query marker FASTA was written to GCF_009696375.1_ASM969637v1_genomic.fna/markers.fasta
[2024-01-24 12:40:47,805] [INFO] Task started: Blastn
[2024-01-24 12:40:47,805] [INFO] Running command: blastn -query GCF_009696375.1_ASM969637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d235c93-b153-47b8-b7fc-4a23b198302c/dqc_reference/reference_markers.fasta -out GCF_009696375.1_ASM969637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:48,443] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:48,447] [INFO] Selected 19 target genomes.
[2024-01-24 12:40:48,448] [INFO] Target genome list was writen to GCF_009696375.1_ASM969637v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:48,455] [INFO] Task started: fastANI
[2024-01-24 12:40:48,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fe10c8a-04ce-4989-b8c5-b229d34a5531/GCF_009696375.1_ASM969637v1_genomic.fna.gz --refList GCF_009696375.1_ASM969637v1_genomic.fna/target_genomes.txt --output GCF_009696375.1_ASM969637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:03,644] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:03,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d235c93-b153-47b8-b7fc-4a23b198302c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:03,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d235c93-b153-47b8-b7fc-4a23b198302c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:03,661] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:41:03,662] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:03,662] [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
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	100.0	1368	1370	95	conclusive
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	84.4356	138	1370	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	81.7722	112	1370	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	79.7098	346	1370	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	79.6147	355	1370	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	79.1683	343	1370	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	79.1678	339	1370	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	79.0758	338	1370	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	78.7535	334	1370	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	78.3593	53	1370	95	below_threshold
Lachnoclostridium pacaense	strain=Marseille-P3100	GCA_900566185.1	1917870	1917870	type	True	78.0161	110	1370	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.7443	170	1370	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.9176	86	1370	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.8956	93	1370	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.8803	87	1370	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.8343	92	1370	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	76.6488	81	1370	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:03,663] [INFO] DFAST Taxonomy check result was written to GCF_009696375.1_ASM969637v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:03,664] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:03,664] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:03,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d235c93-b153-47b8-b7fc-4a23b198302c/dqc_reference/checkm_data
[2024-01-24 12:41:03,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:03,706] [INFO] Task started: CheckM
[2024-01-24 12:41:03,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696375.1_ASM969637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696375.1_ASM969637v1_genomic.fna/checkm_input GCF_009696375.1_ASM969637v1_genomic.fna/checkm_result
[2024-01-24 12:41:38,203] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:38,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:38,224] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:38,224] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:38,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696375.1_ASM969637v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:38,225] [INFO] Task started: Blastn
[2024-01-24 12:41:38,225] [INFO] Running command: blastn -query GCF_009696375.1_ASM969637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d235c93-b153-47b8-b7fc-4a23b198302c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696375.1_ASM969637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:39,234] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:39,237] [INFO] Selected 17 target genomes.
[2024-01-24 12:41:39,237] [INFO] Target genome list was writen to GCF_009696375.1_ASM969637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:39,249] [INFO] Task started: fastANI
[2024-01-24 12:41:39,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fe10c8a-04ce-4989-b8c5-b229d34a5531/GCF_009696375.1_ASM969637v1_genomic.fna.gz --refList GCF_009696375.1_ASM969637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696375.1_ASM969637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:53,191] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:53,211] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:53,211] [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_009696375.1	s__Enterocloster porci	100.0	1368	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.46	99.31	0.94	0.93	5	conclusive
GCA_001304855.1	s__Enterocloster sp001304855	80.4556	555	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002160535.1	s__Clostridium_Q saccharolyticum_A	79.6127	116	1370	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	-
GCF_002234575.2	s__Enterocloster bolteae	79.1954	337	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.46	96.97	0.88	0.78	35	-
GCF_000233455.1	s__Enterocloster citroniae	79.1296	339	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.23	99.13	0.87	0.84	10	-
GCF_000424325.1	s__Enterocloster clostridioformis_A	79.0986	348	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.02	99.02	0.92	0.92	2	-
GCA_000155435.1	s__Enterocloster sp000155435	78.9286	301	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.08	98.70	0.90	0.83	5	-
GCF_005845215.1	s__Enterocloster sp005845215	78.927	338	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.62	99.13	0.95	0.86	6	-
GCF_900113155.1	s__Enterocloster clostridioformis	78.7535	334	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.82	97.34	0.84	0.75	45	-
GCF_000466485.1	s__Clostridium_Q symbiosum	78.4738	94	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.86	98.57	0.86	0.81	32	-
GCF_003434055.1	s__Enterocloster aldenensis	78.3561	310	1370	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_900547035.1	s__Enterocloster excrementigallinarum	76.8825	140	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
GCF_900626075.1	s__Clostridium_Q transplantifaecale	76.7669	79	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002899675.1	s__CHH4-2 sp002899675	76.747	87	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_019114305.1	s__Hungatella pullicola	76.5578	69	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	99.96	99.96	0.96	0.96	2	-
GCA_900540335.1	s__Ventrimonas sp900540335	76.429	94	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_002365025.1	s__Lacrimispora sp002365025	76.0317	79	1370	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.9912	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:53,213] [INFO] GTDB search result was written to GCF_009696375.1_ASM969637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:53,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:53,221] [INFO] DFAST_QC result json was written to GCF_009696375.1_ASM969637v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:53,221] [INFO] DFAST_QC completed!
[2024-01-24 12:41:53,221] [INFO] Total running time: 0h1m17s