[2023-06-29 04:41:39,190] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:41:39,199] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:41:39,199] [INFO] DQC Reference Directory: /var/lib/cwl/stga0e77421-2e66-444b-94f6-d664da030109/dqc_reference
[2023-06-29 04:41:42,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:41:42,377] [INFO] Task started: Prodigal
[2023-06-29 04:41:42,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg7333436d-6cea-4d2d-a30f-ec5f23bbbb1b/GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:41:49,279] [INFO] Task succeeded: Prodigal
[2023-06-29 04:41:49,280] [INFO] Task started: HMMsearch
[2023-06-29 04:41:49,280] [INFO] Running command: hmmsearch --tblout GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0e77421-2e66-444b-94f6-d664da030109/dqc_reference/reference_markers.hmm GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:41:49,530] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:41:49,532] [INFO] Found 6/6 markers.
[2023-06-29 04:41:49,562] [INFO] Query marker FASTA was written to GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 04:41:49,563] [INFO] Task started: Blastn
[2023-06-29 04:41:49,563] [INFO] Running command: blastn -query GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga0e77421-2e66-444b-94f6-d664da030109/dqc_reference/reference_markers.fasta -out GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:41:50,231] [INFO] Task succeeded: Blastn
[2023-06-29 04:41:50,234] [INFO] Selected 12 target genomes.
[2023-06-29 04:41:50,235] [INFO] Target genome list was writen to GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 04:41:50,237] [INFO] Task started: fastANI
[2023-06-29 04:41:50,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg7333436d-6cea-4d2d-a30f-ec5f23bbbb1b/GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:41:57,287] [INFO] Task succeeded: fastANI
[2023-06-29 04:41:57,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0e77421-2e66-444b-94f6-d664da030109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:41:57,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0e77421-2e66-444b-94f6-d664da030109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:41:57,297] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:41:57,297] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:41:57,297] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.3179	322	778	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.0883	183	778	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.0212	205	778	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.6441	107	778	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.4354	116	778	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.3468	104	778	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.3248	151	778	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.1881	128	778	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.0731	98	778	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.0164	95	778	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:41:57,299] [INFO] DFAST Taxonomy check result was written to GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 04:41:57,300] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:41:57,300] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:41:57,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0e77421-2e66-444b-94f6-d664da030109/dqc_reference/checkm_data
[2023-06-29 04:41:57,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:41:57,339] [INFO] Task started: CheckM
[2023-06-29 04:41:57,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 04:42:24,099] [INFO] Task succeeded: CheckM
[2023-06-29 04:42:24,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:42:24,124] [INFO] ===== Completeness check finished =====
[2023-06-29 04:42:24,124] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:42:24,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 04:42:24,125] [INFO] Task started: Blastn
[2023-06-29 04:42:24,125] [INFO] Running command: blastn -query GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga0e77421-2e66-444b-94f6-d664da030109/dqc_reference/reference_markers_gtdb.fasta -out GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:42:25,309] [INFO] Task succeeded: Blastn
[2023-06-29 04:42:25,313] [INFO] Selected 19 target genomes.
[2023-06-29 04:42:25,313] [INFO] Target genome list was writen to GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:42:25,332] [INFO] Task started: fastANI
[2023-06-29 04:42:25,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg7333436d-6cea-4d2d-a30f-ec5f23bbbb1b/GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:42:35,914] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:35,934] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 04:42:35,934] [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_910584995.1	s__Dysosmobacter sp910584995	99.0637	719	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014799855.1	s__Dysosmobacter sp014799855	81.9742	317	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403435.2	s__Dysosmobacter sp000403435	80.29	404	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.32	98.32	0.80	0.80	2	-
GCA_910585385.1	s__Dysosmobacter sp910585385	80.2297	339	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544955.1	s__Dysosmobacter sp900544955	80.1253	309	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574635.1	s__Dysosmobacter sp009774015	80.0878	396	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	96.89	96.54	0.80	0.71	5	-
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	79.9409	306	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587875.1	s__Dysosmobacter sp910587875	79.8484	333	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587705.1	s__Dysosmobacter sp910587705	79.7634	364	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773995.1	s__Dysosmobacter sp009773995	79.752	335	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.84	99.84	0.82	0.82	2	-
GCA_910584075.1	s__Dysosmobacter sp910584075	79.7238	356	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	79.6382	303	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575505.1	s__Dysosmobacter sp910575505	79.3503	370	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937405.1	s__Dysosmobacter sp017937405	79.2296	283	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904393855.1	s__Dysosmobacter sp904393855	79.2091	214	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588005.1	s__Dysosmobacter sp910588005	79.0618	307	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585815.1	s__Lawsonibacter sp910585815	77.6906	151	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911595.1	s__Lawsonibacter sp009911595	77.6556	164	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579595.1	s__Enterenecus sp910579595	77.4908	124	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:42:35,936] [INFO] GTDB search result was written to GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 04:42:35,937] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:42:35,941] [INFO] DFAST_QC result json was written to GCA_948441575.1_SRR17684615_bin.10_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 04:42:35,941] [INFO] DFAST_QC completed!
[2023-06-29 04:42:35,941] [INFO] Total running time: 0h0m57s