[2024-01-25 19:31:51,360] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,361] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg46d6eeaa-5d90-4cda-9629-ac9e27053b7e/dqc_reference
[2024-01-25 19:31:52,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,482] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,482] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc905ee3-805b-4ea4-9867-76652279ff16/GCF_014385025.1_ASM1438502v1_genomic.fna.gz | prodigal -d GCF_014385025.1_ASM1438502v1_genomic.fna/cds.fna -a GCF_014385025.1_ASM1438502v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:00,111] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:00,111] [INFO] Task started: HMMsearch
[2024-01-25 19:32:00,111] [INFO] Running command: hmmsearch --tblout GCF_014385025.1_ASM1438502v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46d6eeaa-5d90-4cda-9629-ac9e27053b7e/dqc_reference/reference_markers.hmm GCF_014385025.1_ASM1438502v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:00,345] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:00,346] [INFO] Found 6/6 markers.
[2024-01-25 19:32:00,372] [INFO] Query marker FASTA was written to GCF_014385025.1_ASM1438502v1_genomic.fna/markers.fasta
[2024-01-25 19:32:00,373] [INFO] Task started: Blastn
[2024-01-25 19:32:00,373] [INFO] Running command: blastn -query GCF_014385025.1_ASM1438502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d6eeaa-5d90-4cda-9629-ac9e27053b7e/dqc_reference/reference_markers.fasta -out GCF_014385025.1_ASM1438502v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:00,996] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:01,000] [INFO] Selected 23 target genomes.
[2024-01-25 19:32:01,000] [INFO] Target genome list was writen to GCF_014385025.1_ASM1438502v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:01,008] [INFO] Task started: fastANI
[2024-01-25 19:32:01,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc905ee3-805b-4ea4-9867-76652279ff16/GCF_014385025.1_ASM1438502v1_genomic.fna.gz --refList GCF_014385025.1_ASM1438502v1_genomic.fna/target_genomes.txt --output GCF_014385025.1_ASM1438502v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:15,339] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:15,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46d6eeaa-5d90-4cda-9629-ac9e27053b7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:15,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46d6eeaa-5d90-4cda-9629-ac9e27053b7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:15,346] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:32:15,346] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:32:15,346] [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
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	81.6065	120	1044	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_025146135.1	169435	169435	type	True	80.3475	73	1044	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	80.2675	75	1044	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	78.4821	84	1044	95	below_threshold
Provencibacterium massiliense	strain=Marseille-P2780	GCA_900169495.1	1841868	1841868	type	True	78.2744	116	1044	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.6282	121	1044	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:15,347] [INFO] DFAST Taxonomy check result was written to GCF_014385025.1_ASM1438502v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:15,348] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:15,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:15,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46d6eeaa-5d90-4cda-9629-ac9e27053b7e/dqc_reference/checkm_data
[2024-01-25 19:32:15,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:15,382] [INFO] Task started: CheckM
[2024-01-25 19:32:15,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014385025.1_ASM1438502v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014385025.1_ASM1438502v1_genomic.fna/checkm_input GCF_014385025.1_ASM1438502v1_genomic.fna/checkm_result
[2024-01-25 19:32:41,235] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:41,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:41,255] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:41,255] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:41,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014385025.1_ASM1438502v1_genomic.fna/markers.fasta)
[2024-01-25 19:32:41,256] [INFO] Task started: Blastn
[2024-01-25 19:32:41,256] [INFO] Running command: blastn -query GCF_014385025.1_ASM1438502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d6eeaa-5d90-4cda-9629-ac9e27053b7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014385025.1_ASM1438502v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:42,413] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:42,418] [INFO] Selected 20 target genomes.
[2024-01-25 19:32:42,418] [INFO] Target genome list was writen to GCF_014385025.1_ASM1438502v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:42,431] [INFO] Task started: fastANI
[2024-01-25 19:32:42,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc905ee3-805b-4ea4-9867-76652279ff16/GCF_014385025.1_ASM1438502v1_genomic.fna.gz --refList GCF_014385025.1_ASM1438502v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014385025.1_ASM1438502v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:52,243] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:52,250] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:52,250] [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_014385025.1	s__Fimivivens sp014385025	100.0	1038	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fimivivens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900113995.1	s__Fimivivens sp900113995	94.047	720	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fimivivens	95.0	99.55	99.49	0.95	0.93	4	-
GCA_014384885.1	s__Hydrogenoanaerobacterium sp014384885	81.6308	119	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	98.59	98.59	0.91	0.91	2	-
GCF_000154565.1	s__Anaerotruncus colihominis	80.3081	74	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.95	97.75	0.87	0.80	16	-
GCF_900078395.1	s__Anaerotruncus rubiinfantis	78.5312	83	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.23	99.21	0.89	0.86	5	-
GCF_900199635.1	s__Anaerotruncus massiliensis	77.6271	121	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCF_010206195.1	s__Anaerotruncus colihominis_A	77.3588	66	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.98	98.75	0.89	0.87	3	-
GCA_018716105.1	s__Fimivivens faecavium	77.2334	91	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fimivivens	95.0	99.67	99.42	0.92	0.91	3	-
GCA_017399785.1	s__Fimivivens sp017399785	76.8648	60	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fimivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760305.1	s__UMGS856 sp900760305	76.1491	55	1044	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS856	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:52,252] [INFO] GTDB search result was written to GCF_014385025.1_ASM1438502v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:52,253] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:52,256] [INFO] DFAST_QC result json was written to GCF_014385025.1_ASM1438502v1_genomic.fna/dqc_result.json
[2024-01-25 19:32:52,256] [INFO] DFAST_QC completed!
[2024-01-25 19:32:52,256] [INFO] Total running time: 0h1m1s