[2023-06-28 03:12:14,207] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:12:14,211] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:12:14,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d56ff1b-93b1-4ede-82bd-6082d6c905f3/dqc_reference
[2023-06-28 03:12:16,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:12:16,442] [INFO] Task started: Prodigal
[2023-06-28 03:12:16,443] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c607a30-f2e7-475b-b7cf-ab2e9cf6a9d0/GCA_944384005.1_BRZ_CH_bin70_genomic.fna.gz | prodigal -d GCA_944384005.1_BRZ_CH_bin70_genomic.fna/cds.fna -a GCA_944384005.1_BRZ_CH_bin70_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:12:23,770] [INFO] Task succeeded: Prodigal
[2023-06-28 03:12:23,770] [INFO] Task started: HMMsearch
[2023-06-28 03:12:23,770] [INFO] Running command: hmmsearch --tblout GCA_944384005.1_BRZ_CH_bin70_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d56ff1b-93b1-4ede-82bd-6082d6c905f3/dqc_reference/reference_markers.hmm GCA_944384005.1_BRZ_CH_bin70_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:12:24,052] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:12:24,054] [INFO] Found 6/6 markers.
[2023-06-28 03:12:24,083] [INFO] Query marker FASTA was written to GCA_944384005.1_BRZ_CH_bin70_genomic.fna/markers.fasta
[2023-06-28 03:12:24,083] [INFO] Task started: Blastn
[2023-06-28 03:12:24,083] [INFO] Running command: blastn -query GCA_944384005.1_BRZ_CH_bin70_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d56ff1b-93b1-4ede-82bd-6082d6c905f3/dqc_reference/reference_markers.fasta -out GCA_944384005.1_BRZ_CH_bin70_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:12:24,731] [INFO] Task succeeded: Blastn
[2023-06-28 03:12:24,736] [INFO] Selected 25 target genomes.
[2023-06-28 03:12:24,736] [INFO] Target genome list was writen to GCA_944384005.1_BRZ_CH_bin70_genomic.fna/target_genomes.txt
[2023-06-28 03:12:24,738] [INFO] Task started: fastANI
[2023-06-28 03:12:24,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c607a30-f2e7-475b-b7cf-ab2e9cf6a9d0/GCA_944384005.1_BRZ_CH_bin70_genomic.fna.gz --refList GCA_944384005.1_BRZ_CH_bin70_genomic.fna/target_genomes.txt --output GCA_944384005.1_BRZ_CH_bin70_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:12:40,686] [INFO] Task succeeded: fastANI
[2023-06-28 03:12:40,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d56ff1b-93b1-4ede-82bd-6082d6c905f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:12:40,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d56ff1b-93b1-4ede-82bd-6082d6c905f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:12:40,701] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:12:40,701] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 03:12:40,702] [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 asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	78.46	263	884	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	78.437	259	884	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	78.004	267	884	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	77.9597	133	884	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	77.9591	270	884	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	77.9009	270	884	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	77.8992	250	884	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	77.8477	247	884	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	77.8226	247	884	95	below_threshold
Lachnoclostridium pacaense	strain=Marseille-P3100	GCA_900566185.1	1917870	1917870	type	True	77.7121	88	884	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	77.0255	82	884	95	below_threshold
Cuneatibacter caecimuris	strain=DSM 29486	GCA_004216775.1	1796618	1796618	type	True	76.9887	52	884	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.9486	90	884	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	76.7733	50	884	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	76.4283	54	884	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.1102	57	884	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 03:12:40,704] [INFO] DFAST Taxonomy check result was written to GCA_944384005.1_BRZ_CH_bin70_genomic.fna/tc_result.tsv
[2023-06-28 03:12:40,704] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:12:40,705] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:12:40,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d56ff1b-93b1-4ede-82bd-6082d6c905f3/dqc_reference/checkm_data
[2023-06-28 03:12:40,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:12:40,741] [INFO] Task started: CheckM
[2023-06-28 03:12:40,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944384005.1_BRZ_CH_bin70_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944384005.1_BRZ_CH_bin70_genomic.fna/checkm_input GCA_944384005.1_BRZ_CH_bin70_genomic.fna/checkm_result
[2023-06-28 03:13:08,668] [INFO] Task succeeded: CheckM
[2023-06-28 03:13:08,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:13:08,696] [INFO] ===== Completeness check finished =====
[2023-06-28 03:13:08,697] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:13:08,697] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944384005.1_BRZ_CH_bin70_genomic.fna/markers.fasta)
[2023-06-28 03:13:08,697] [INFO] Task started: Blastn
[2023-06-28 03:13:08,697] [INFO] Running command: blastn -query GCA_944384005.1_BRZ_CH_bin70_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d56ff1b-93b1-4ede-82bd-6082d6c905f3/dqc_reference/reference_markers_gtdb.fasta -out GCA_944384005.1_BRZ_CH_bin70_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:13:09,759] [INFO] Task succeeded: Blastn
[2023-06-28 03:13:09,765] [INFO] Selected 21 target genomes.
[2023-06-28 03:13:09,765] [INFO] Target genome list was writen to GCA_944384005.1_BRZ_CH_bin70_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:13:09,778] [INFO] Task started: fastANI
[2023-06-28 03:13:09,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c607a30-f2e7-475b-b7cf-ab2e9cf6a9d0/GCA_944384005.1_BRZ_CH_bin70_genomic.fna.gz --refList GCA_944384005.1_BRZ_CH_bin70_genomic.fna/target_genomes_gtdb.txt --output GCA_944384005.1_BRZ_CH_bin70_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:13:24,443] [INFO] Task succeeded: fastANI
[2023-06-28 03:13:24,462] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 03:13:24,462] [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_019119575.1	s__Enterocloster excrementipullorum	99.2025	805	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.43	99.23	0.94	0.92	5	conclusive
GCF_902364025.1	s__Enterocloster lavalensis	78.7565	250	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.58	98.12	0.90	0.83	6	-
GCA_018380885.1	s__Enterocloster sp900555905	78.4429	255	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
GCF_000158075.1	s__Enterocloster asparagiformis	78.4429	258	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	-
GCA_900753815.1	s__Enterocloster sp900753815	78.2494	175	884	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_900770345.1	s__Enterocloster sp900770345	78.2493	226	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005845215.1	s__Enterocloster sp005845215	78.0176	254	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.62	99.13	0.95	0.86	6	-
GCA_900547035.1	s__Enterocloster excrementigallinarum	78.0116	224	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
GCA_019118585.1	s__Enterocloster faecavium	77.9787	209	884	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_002234575.2	s__Enterocloster bolteae	77.9707	268	884	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_009696375.1	s__Enterocloster porci	77.9389	132	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.46	99.31	0.94	0.93	5	-
GCA_000155435.1	s__Enterocloster sp000155435	77.8838	227	884	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_000424325.1	s__Enterocloster clostridioformis_A	77.803	244	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.02	99.02	0.92	0.92	2	-
GCF_000233455.1	s__Enterocloster citroniae	77.6871	242	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.23	99.13	0.87	0.84	10	-
GCA_019114845.1	s__Lachnoclostridium_A stercoripullorum	77.6804	167	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
GCF_001517625.2	s__Enterocloster sp001517625	77.5724	200	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.90	98.46	0.89	0.80	9	-
GCA_900549235.1	s__Enterocloster sp900549235	77.5143	223	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.03	99.00	0.79	0.77	3	-
GCA_900759225.1	s__Enterocloster sp900759225	77.3192	141	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.23	98.23	0.78	0.78	2	-
GCA_018223375.1	s__Clostridium_Q sp000435655	77.161	91	884	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.36	96.90	0.90	0.85	8	-
GCF_000466485.1	s__Clostridium_Q symbiosum	76.7988	63	884	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	-
GCA_018377235.1	s__Clostridium_Q sp018377235	76.6504	67	884	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	-
--------------------------------------------------------------------------------
[2023-06-28 03:13:24,464] [INFO] GTDB search result was written to GCA_944384005.1_BRZ_CH_bin70_genomic.fna/result_gtdb.tsv
[2023-06-28 03:13:24,465] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:13:24,469] [INFO] DFAST_QC result json was written to GCA_944384005.1_BRZ_CH_bin70_genomic.fna/dqc_result.json
[2023-06-28 03:13:24,470] [INFO] DFAST_QC completed!
[2023-06-28 03:13:24,470] [INFO] Total running time: 0h1m10s