[2024-01-25 18:14:05,581] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,584] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1f236b2-4f54-4785-8a57-18ccfb424460/dqc_reference
[2024-01-25 18:14:06,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:06,758] [INFO] Task started: Prodigal
[2024-01-25 18:14:06,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg77158bbd-a8e6-4e3b-be1d-967098346c28/GCF_022453685.1_ASM2245368v1_genomic.fna.gz | prodigal -d GCF_022453685.1_ASM2245368v1_genomic.fna/cds.fna -a GCF_022453685.1_ASM2245368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:14,277] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:14,277] [INFO] Task started: HMMsearch
[2024-01-25 18:14:14,277] [INFO] Running command: hmmsearch --tblout GCF_022453685.1_ASM2245368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1f236b2-4f54-4785-8a57-18ccfb424460/dqc_reference/reference_markers.hmm GCF_022453685.1_ASM2245368v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:14,496] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:14,497] [INFO] Found 6/6 markers.
[2024-01-25 18:14:14,525] [INFO] Query marker FASTA was written to GCF_022453685.1_ASM2245368v1_genomic.fna/markers.fasta
[2024-01-25 18:14:14,525] [INFO] Task started: Blastn
[2024-01-25 18:14:14,525] [INFO] Running command: blastn -query GCF_022453685.1_ASM2245368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1f236b2-4f54-4785-8a57-18ccfb424460/dqc_reference/reference_markers.fasta -out GCF_022453685.1_ASM2245368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:15,106] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:15,108] [INFO] Selected 30 target genomes.
[2024-01-25 18:14:15,109] [INFO] Target genome list was writen to GCF_022453685.1_ASM2245368v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:15,123] [INFO] Task started: fastANI
[2024-01-25 18:14:15,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg77158bbd-a8e6-4e3b-be1d-967098346c28/GCF_022453685.1_ASM2245368v1_genomic.fna.gz --refList GCF_022453685.1_ASM2245368v1_genomic.fna/target_genomes.txt --output GCF_022453685.1_ASM2245368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:30,089] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:30,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1f236b2-4f54-4785-8a57-18ccfb424460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:30,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1f236b2-4f54-4785-8a57-18ccfb424460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:30,099] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:14:30,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:14:30,100] [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 comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	83.1272	114	1150	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	82.963	81	1150	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	81.5079	158	1150	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	81.3886	136	1150	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	81.0594	95	1150	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	81.0512	169	1150	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	80.6007	202	1150	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	80.5375	73	1150	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	80.528	151	1150	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	80.5257	96	1150	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	80.0048	70	1150	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.7708	146	1150	95	below_threshold
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	77.8746	91	1150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:30,101] [INFO] DFAST Taxonomy check result was written to GCF_022453685.1_ASM2245368v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:30,101] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:30,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:30,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1f236b2-4f54-4785-8a57-18ccfb424460/dqc_reference/checkm_data
[2024-01-25 18:14:30,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:30,138] [INFO] Task started: CheckM
[2024-01-25 18:14:30,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022453685.1_ASM2245368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022453685.1_ASM2245368v1_genomic.fna/checkm_input GCF_022453685.1_ASM2245368v1_genomic.fna/checkm_result
[2024-01-25 18:14:56,585] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:56,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:56,605] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:56,606] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:56,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022453685.1_ASM2245368v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:56,606] [INFO] Task started: Blastn
[2024-01-25 18:14:56,606] [INFO] Running command: blastn -query GCF_022453685.1_ASM2245368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1f236b2-4f54-4785-8a57-18ccfb424460/dqc_reference/reference_markers_gtdb.fasta -out GCF_022453685.1_ASM2245368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:57,577] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:57,579] [INFO] Selected 14 target genomes.
[2024-01-25 18:14:57,580] [INFO] Target genome list was writen to GCF_022453685.1_ASM2245368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:57,591] [INFO] Task started: fastANI
[2024-01-25 18:14:57,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg77158bbd-a8e6-4e3b-be1d-967098346c28/GCF_022453685.1_ASM2245368v1_genomic.fna.gz --refList GCF_022453685.1_ASM2245368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022453685.1_ASM2245368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:05,507] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:05,516] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:05,516] [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_000020605.1	s__Agathobacter rectalis	99.9926	1143	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.37	96.06	0.82	0.65	151	conclusive
GCA_900546625.1	s__Agathobacter sp900546625	94.5554	743	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	96.96	96.96	0.86	0.86	2	-
GCA_900317585.1	s__Agathobacter sp900317585	94.4291	638	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.18	95.52	0.87	0.83	5	-
GCA_905209075.1	s__Agathobacter sp905209075	81.8162	331	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.22	97.67	0.80	0.73	5	-
GCA_900549895.1	s__Agathobacter sp900549895	78.9397	97	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552085.1	s__Agathobacter sp900552085	78.8098	126	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_900548765.1	s__Agathobacter sp900548765	78.5413	175	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	97.03	0.78	0.78	2	-
GCA_017937095.1	s__Roseburia sp017937095	78.1051	93	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543445.1	s__Agathobacter sp900543445	78.0269	151	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
GCA_003483745.1	s__Roseburia sp003483745	77.7301	102	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_002299665.1	s__CAG-45 sp002299665	77.3836	55	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587655.1	s__Agathobacter sp910587655	76.975	83	1150	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:05,518] [INFO] GTDB search result was written to GCF_022453685.1_ASM2245368v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:05,518] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:05,521] [INFO] DFAST_QC result json was written to GCF_022453685.1_ASM2245368v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:05,521] [INFO] DFAST_QC completed!
[2024-01-25 18:15:05,521] [INFO] Total running time: 0h0m60s