[2024-01-24 12:13:59,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:59,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:59,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg85d3aa12-bb74-485f-a2ea-97210067b203/dqc_reference
[2024-01-24 12:14:00,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:00,634] [INFO] Task started: Prodigal
[2024-01-24 12:14:00,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg33e06ca2-1c21-4bec-9a0c-bb4b698a751f/GCF_009696005.1_ASM969600v1_genomic.fna.gz | prodigal -d GCF_009696005.1_ASM969600v1_genomic.fna/cds.fna -a GCF_009696005.1_ASM969600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:07,773] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:07,774] [INFO] Task started: HMMsearch
[2024-01-24 12:14:07,774] [INFO] Running command: hmmsearch --tblout GCF_009696005.1_ASM969600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85d3aa12-bb74-485f-a2ea-97210067b203/dqc_reference/reference_markers.hmm GCF_009696005.1_ASM969600v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:08,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:08,080] [INFO] Found 6/6 markers.
[2024-01-24 12:14:08,106] [INFO] Query marker FASTA was written to GCF_009696005.1_ASM969600v1_genomic.fna/markers.fasta
[2024-01-24 12:14:08,107] [INFO] Task started: Blastn
[2024-01-24 12:14:08,107] [INFO] Running command: blastn -query GCF_009696005.1_ASM969600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85d3aa12-bb74-485f-a2ea-97210067b203/dqc_reference/reference_markers.fasta -out GCF_009696005.1_ASM969600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:08,819] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:08,822] [INFO] Selected 24 target genomes.
[2024-01-24 12:14:08,823] [INFO] Target genome list was writen to GCF_009696005.1_ASM969600v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:08,833] [INFO] Task started: fastANI
[2024-01-24 12:14:08,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e06ca2-1c21-4bec-9a0c-bb4b698a751f/GCF_009696005.1_ASM969600v1_genomic.fna.gz --refList GCF_009696005.1_ASM969600v1_genomic.fna/target_genomes.txt --output GCF_009696005.1_ASM969600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:23,882] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:23,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85d3aa12-bb74-485f-a2ea-97210067b203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:23,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85d3aa12-bb74-485f-a2ea-97210067b203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:23,888] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:23,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:23,889] [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
Bilifractor porci	strain=Oil+RF-744-WCA-WT-13	GCA_009696005.1	2606636	2606636	type	True	100.0	892	893	95	conclusive
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	76.6319	71	893	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.2172	57	893	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	76.1776	50	893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:23,890] [INFO] DFAST Taxonomy check result was written to GCF_009696005.1_ASM969600v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:23,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:23,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:23,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85d3aa12-bb74-485f-a2ea-97210067b203/dqc_reference/checkm_data
[2024-01-24 12:14:23,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:23,926] [INFO] Task started: CheckM
[2024-01-24 12:14:23,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696005.1_ASM969600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696005.1_ASM969600v1_genomic.fna/checkm_input GCF_009696005.1_ASM969600v1_genomic.fna/checkm_result
[2024-01-24 12:14:51,213] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:51,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:51,234] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:51,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:51,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696005.1_ASM969600v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:51,235] [INFO] Task started: Blastn
[2024-01-24 12:14:51,235] [INFO] Running command: blastn -query GCF_009696005.1_ASM969600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85d3aa12-bb74-485f-a2ea-97210067b203/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696005.1_ASM969600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:52,310] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:52,314] [INFO] Selected 22 target genomes.
[2024-01-24 12:14:52,314] [INFO] Target genome list was writen to GCF_009696005.1_ASM969600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:52,391] [INFO] Task started: fastANI
[2024-01-24 12:14:52,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e06ca2-1c21-4bec-9a0c-bb4b698a751f/GCF_009696005.1_ASM969600v1_genomic.fna.gz --refList GCF_009696005.1_ASM969600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696005.1_ASM969600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:03,842] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:03,853] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:03,854] [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_009696005.1	s__Bilifractor porci	100.0	892	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	98.26	98.26	0.83	0.83	2	conclusive
GCA_902756775.1	s__Bilifractor sp900317175	89.9782	484	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	97.95	96.99	0.76	0.63	20	-
GCA_002394235.1	s__Bilifractor sp002394235	78.0103	125	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	99.06	98.97	0.80	0.76	4	-
GCA_900314295.1	s__Bilifractor sp900314295	77.5195	121	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	99.31	99.31	0.88	0.88	2	-
GCF_000621585.1	s__Bilifractor cellulosolvens_A	77.2707	79	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770225.1	s__Bilifractor sp900770225	77.0853	89	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318405.1	s__Bilifractor sp900318405	76.9889	90	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	99.33	99.23	0.95	0.94	3	-
GCA_018716575.1	s__Scatomonas merdavium	76.895	72	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	98.69	98.69	0.82	0.82	2	-
GCA_017887445.1	s__Fusicatenibacter sp017887445	76.7698	61	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713515.1	s__Scatomonas pullistercoris	76.6919	85	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.97	99.97	0.94	0.94	2	-
GCA_018711275.1	s__Pullilachnospira intestinigallinarum	76.6209	55	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	99.92	99.92	0.90	0.90	2	-
GCA_002368795.1	s__Bilifractor sp002368795	76.495	90	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201705.1	s__Marvinbryantia sp900550755	75.9071	54	893	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.85	99.71	0.93	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:03,855] [INFO] GTDB search result was written to GCF_009696005.1_ASM969600v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:03,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:03,859] [INFO] DFAST_QC result json was written to GCF_009696005.1_ASM969600v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:03,859] [INFO] DFAST_QC completed!
[2024-01-24 12:15:03,859] [INFO] Total running time: 0h1m5s