[2024-01-24 14:06:59,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:59,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:59,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg86e144cf-02f4-4c57-8537-8cc1b1392df0/dqc_reference
[2024-01-24 14:07:00,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:00,900] [INFO] Task started: Prodigal
[2024-01-24 14:07:00,900] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e1d1828-c4df-4d39-9a0d-a87cbde1a23c/GCF_002051585.1_ASM205158v1_genomic.fna.gz | prodigal -d GCF_002051585.1_ASM205158v1_genomic.fna/cds.fna -a GCF_002051585.1_ASM205158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:12,160] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:12,160] [INFO] Task started: HMMsearch
[2024-01-24 14:07:12,160] [INFO] Running command: hmmsearch --tblout GCF_002051585.1_ASM205158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86e144cf-02f4-4c57-8537-8cc1b1392df0/dqc_reference/reference_markers.hmm GCF_002051585.1_ASM205158v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:12,413] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:12,415] [INFO] Found 6/6 markers.
[2024-01-24 14:07:12,459] [INFO] Query marker FASTA was written to GCF_002051585.1_ASM205158v1_genomic.fna/markers.fasta
[2024-01-24 14:07:12,460] [INFO] Task started: Blastn
[2024-01-24 14:07:12,460] [INFO] Running command: blastn -query GCF_002051585.1_ASM205158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86e144cf-02f4-4c57-8537-8cc1b1392df0/dqc_reference/reference_markers.fasta -out GCF_002051585.1_ASM205158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:13,111] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:13,114] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:13,115] [INFO] Target genome list was writen to GCF_002051585.1_ASM205158v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:13,125] [INFO] Task started: fastANI
[2024-01-24 14:07:13,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e1d1828-c4df-4d39-9a0d-a87cbde1a23c/GCF_002051585.1_ASM205158v1_genomic.fna.gz --refList GCF_002051585.1_ASM205158v1_genomic.fna/target_genomes.txt --output GCF_002051585.1_ASM205158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:22,630] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:22,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86e144cf-02f4-4c57-8537-8cc1b1392df0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:22,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86e144cf-02f4-4c57-8537-8cc1b1392df0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:22,640] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:22,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:22,640] [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 hungatei	strain=DSM 14427	GCA_002051585.1	48256	48256	type	True	100.0	1587	1589	95	conclusive
Ruminiclostridium cellobioparum subsp. termitidis	strain=CT1112	GCA_000350485.1	29371	29355	type	True	79.3693	591	1589	95	below_threshold
Ruminiclostridium cellobioparum	strain=ATCC 15832	GCA_000621505.1	29355	29355	type	True	79.3033	596	1589	95	below_threshold
Ruminiclostridium papyrosolvens	strain=DSM 2782	GCA_000175795.2	29362	29362	type	True	78.3741	197	1589	95	below_threshold
Ruminiclostridium cellulolyticum	strain=H10; ATCC 35319	GCA_000022065.1	1521	1521	type	True	78.3632	184	1589	95	below_threshold
Ruminiclostridium josui	strain=JCM 17888	GCA_001311015.1	1499	1499	type	True	77.7589	185	1589	95	below_threshold
Ruminiclostridium josui	strain=JCM 17888	GCA_000526495.1	1499	1499	type	True	77.7506	190	1589	95	below_threshold
Pseudobacteroides cellulosolvens	strain=DSM 2933	GCA_001262605.1	35825	35825	type	True	76.2245	65	1589	95	below_threshold
Pseudobacteroides cellulosolvens	strain=DSM 2933	GCA_000745845.1	35825	35825	type	True	76.0554	63	1589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:22,642] [INFO] DFAST Taxonomy check result was written to GCF_002051585.1_ASM205158v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:22,642] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:22,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:22,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86e144cf-02f4-4c57-8537-8cc1b1392df0/dqc_reference/checkm_data
[2024-01-24 14:07:22,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:22,690] [INFO] Task started: CheckM
[2024-01-24 14:07:22,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002051585.1_ASM205158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002051585.1_ASM205158v1_genomic.fna/checkm_input GCF_002051585.1_ASM205158v1_genomic.fna/checkm_result
[2024-01-24 14:08:00,349] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:00,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:00,376] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:00,376] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:00,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002051585.1_ASM205158v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:00,377] [INFO] Task started: Blastn
[2024-01-24 14:08:00,377] [INFO] Running command: blastn -query GCF_002051585.1_ASM205158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86e144cf-02f4-4c57-8537-8cc1b1392df0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002051585.1_ASM205158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:01,429] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:01,433] [INFO] Selected 15 target genomes.
[2024-01-24 14:08:01,433] [INFO] Target genome list was writen to GCF_002051585.1_ASM205158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:01,458] [INFO] Task started: fastANI
[2024-01-24 14:08:01,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e1d1828-c4df-4d39-9a0d-a87cbde1a23c/GCF_002051585.1_ASM205158v1_genomic.fna.gz --refList GCF_002051585.1_ASM205158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002051585.1_ASM205158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:13,464] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:13,473] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:13,473] [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_002051585.1	s__Ruminiclostridium hungatei	100.0	1586	1589	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_000350485.1	s__Ruminiclostridium termitidis	79.3695	591	1589	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_000621505.1	s__Ruminiclostridium cellobioparum	79.304	595	1589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	96.6072	98.83	98.83	0.92	0.92	2	-
GCF_000175795.2	s__Ruminiclostridium papyrosolvens	78.3932	195	1589	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_000022065.1	s__Ruminiclostridium cellulolyticum	78.3632	184	1589	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_000244875.1	s__Ruminiclostridium sp000244875	77.9452	219	1589	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_000526495.1	s__Ruminiclostridium josui	77.7712	188	1589	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_001262605.1	s__Pseudobacteroides cellulosolvens	76.2245	65	1589	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 14:08:13,475] [INFO] GTDB search result was written to GCF_002051585.1_ASM205158v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:13,475] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:13,478] [INFO] DFAST_QC result json was written to GCF_002051585.1_ASM205158v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:13,479] [INFO] DFAST_QC completed!
[2024-01-24 14:08:13,479] [INFO] Total running time: 0h1m14s