[2024-01-24 13:45:59,741] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:59,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:59,743] [INFO] DQC Reference Directory: /var/lib/cwl/stga0bfc95e-e7cd-4bc9-8a86-62aa81f92355/dqc_reference
[2024-01-24 13:46:01,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:01,011] [INFO] Task started: Prodigal
[2024-01-24 13:46:01,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a34fa1a-ab43-4b86-9789-75c4a754a30e/GCF_005473905.2_ASM547390v2_genomic.fna.gz | prodigal -d GCF_005473905.2_ASM547390v2_genomic.fna/cds.fna -a GCF_005473905.2_ASM547390v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:09,883] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:09,883] [INFO] Task started: HMMsearch
[2024-01-24 13:46:09,884] [INFO] Running command: hmmsearch --tblout GCF_005473905.2_ASM547390v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0bfc95e-e7cd-4bc9-8a86-62aa81f92355/dqc_reference/reference_markers.hmm GCF_005473905.2_ASM547390v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:10,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:10,175] [INFO] Found 6/6 markers.
[2024-01-24 13:46:10,215] [INFO] Query marker FASTA was written to GCF_005473905.2_ASM547390v2_genomic.fna/markers.fasta
[2024-01-24 13:46:10,216] [INFO] Task started: Blastn
[2024-01-24 13:46:10,216] [INFO] Running command: blastn -query GCF_005473905.2_ASM547390v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga0bfc95e-e7cd-4bc9-8a86-62aa81f92355/dqc_reference/reference_markers.fasta -out GCF_005473905.2_ASM547390v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:10,861] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:10,865] [INFO] Selected 12 target genomes.
[2024-01-24 13:46:10,865] [INFO] Target genome list was writen to GCF_005473905.2_ASM547390v2_genomic.fna/target_genomes.txt
[2024-01-24 13:46:10,888] [INFO] Task started: fastANI
[2024-01-24 13:46:10,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a34fa1a-ab43-4b86-9789-75c4a754a30e/GCF_005473905.2_ASM547390v2_genomic.fna.gz --refList GCF_005473905.2_ASM547390v2_genomic.fna/target_genomes.txt --output GCF_005473905.2_ASM547390v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:20,567] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:20,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0bfc95e-e7cd-4bc9-8a86-62aa81f92355/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:20,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0bfc95e-e7cd-4bc9-8a86-62aa81f92355/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:20,585] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:20,585] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:20,586] [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
Ruminiclostridium herbifermentans	strain=MA18	GCA_005473905.2	2488810	2488810	type	True	100.0	1605	1605	95	conclusive
Ruminiclostridium josui	strain=JCM 17888	GCA_000526495.1	1499	1499	type	True	79.4343	266	1605	95	below_threshold
Ruminiclostridium cellulolyticum	strain=H10; ATCC 35319	GCA_000022065.1	1521	1521	type	True	79.1976	171	1605	95	below_threshold
Ruminiclostridium sufflavum	strain=DSM 19573	GCA_003208175.1	396504	396504	type	True	79.0673	541	1605	95	below_threshold
Ruminiclostridium josui	strain=JCM 17888	GCA_001311015.1	1499	1499	type	True	79.0075	250	1605	95	below_threshold
Ruminiclostridium hungatei	strain=DSM 14427	GCA_002051585.1	48256	48256	type	True	77.977	152	1605	95	below_threshold
Ruminiclostridium papyrosolvens	strain=DSM 2782	GCA_000175795.2	29362	29362	type	True	77.9448	229	1605	95	below_threshold
Ruminiclostridium cellobioparum subsp. termitidis	strain=CT1112	GCA_000350485.1	29371	29355	type	True	77.2968	148	1605	95	below_threshold
Pseudobacteroides cellulosolvens	strain=DSM 2933	GCA_001262605.1	35825	35825	type	True	76.8886	81	1605	95	below_threshold
Pseudobacteroides cellulosolvens	strain=DSM 2933	GCA_000745845.1	35825	35825	type	True	75.6327	73	1605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:20,587] [INFO] DFAST Taxonomy check result was written to GCF_005473905.2_ASM547390v2_genomic.fna/tc_result.tsv
[2024-01-24 13:46:20,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:20,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:20,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0bfc95e-e7cd-4bc9-8a86-62aa81f92355/dqc_reference/checkm_data
[2024-01-24 13:46:20,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:20,642] [INFO] Task started: CheckM
[2024-01-24 13:46:20,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005473905.2_ASM547390v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005473905.2_ASM547390v2_genomic.fna/checkm_input GCF_005473905.2_ASM547390v2_genomic.fna/checkm_result
[2024-01-24 13:46:52,004] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:52,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:52,026] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:52,027] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:52,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005473905.2_ASM547390v2_genomic.fna/markers.fasta)
[2024-01-24 13:46:52,028] [INFO] Task started: Blastn
[2024-01-24 13:46:52,028] [INFO] Running command: blastn -query GCF_005473905.2_ASM547390v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga0bfc95e-e7cd-4bc9-8a86-62aa81f92355/dqc_reference/reference_markers_gtdb.fasta -out GCF_005473905.2_ASM547390v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:53,047] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:53,050] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:53,050] [INFO] Target genome list was writen to GCF_005473905.2_ASM547390v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:53,160] [INFO] Task started: fastANI
[2024-01-24 13:46:53,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a34fa1a-ab43-4b86-9789-75c4a754a30e/GCF_005473905.2_ASM547390v2_genomic.fna.gz --refList GCF_005473905.2_ASM547390v2_genomic.fna/target_genomes_gtdb.txt --output GCF_005473905.2_ASM547390v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:03,742] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:03,753] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:03,754] [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_005473905.2	s__Ruminiclostridium herbifermentans	100.0	1605	1605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000526495.1	s__Ruminiclostridium josui	79.5111	267	1605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	99.95	99.95	1.00	1.00	2	-
GCF_003208175.1	s__Ruminiclostridium sufflavum	79.0549	542	1605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002051585.1	s__Ruminiclostridium hungatei	77.9846	151	1605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175795.2	s__Ruminiclostridium papyrosolvens	77.9007	230	1605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421965.1	s__Ruminiclostridium papyrosolvens_A	77.8557	196	1605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350485.1	s__Ruminiclostridium termitidis	77.2957	148	1605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	96.6072	N/A	N/A	N/A	N/A	1	-
GCF_001262605.1	s__Pseudobacteroides cellulosolvens	77.17	81	1605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-2933;g__Pseudobacteroides	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:03,755] [INFO] GTDB search result was written to GCF_005473905.2_ASM547390v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:03,756] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:03,759] [INFO] DFAST_QC result json was written to GCF_005473905.2_ASM547390v2_genomic.fna/dqc_result.json
[2024-01-24 13:47:03,760] [INFO] DFAST_QC completed!
[2024-01-24 13:47:03,760] [INFO] Total running time: 0h1m4s