[2023-06-30 18:32:17,495] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:32:17,498] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:32:17,498] [INFO] DQC Reference Directory: /var/lib/cwl/stga3da1836-1f79-41ea-af0d-5a47d82500b6/dqc_reference
[2023-06-30 18:32:18,702] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:32:18,703] [INFO] Task started: Prodigal
[2023-06-30 18:32:18,703] [INFO] Running command: gunzip -c /var/lib/cwl/stgae252e24-b022-4c9c-b72f-c4621c794950/GCA_008671585.1_ASM867158v1_genomic.fna.gz | prodigal -d GCA_008671585.1_ASM867158v1_genomic.fna/cds.fna -a GCA_008671585.1_ASM867158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:32:21,945] [INFO] Task succeeded: Prodigal
[2023-06-30 18:32:21,945] [INFO] Task started: HMMsearch
[2023-06-30 18:32:21,945] [INFO] Running command: hmmsearch --tblout GCA_008671585.1_ASM867158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3da1836-1f79-41ea-af0d-5a47d82500b6/dqc_reference/reference_markers.hmm GCA_008671585.1_ASM867158v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:32:22,174] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:32:22,175] [INFO] Found 6/6 markers.
[2023-06-30 18:32:22,195] [INFO] Query marker FASTA was written to GCA_008671585.1_ASM867158v1_genomic.fna/markers.fasta
[2023-06-30 18:32:22,195] [INFO] Task started: Blastn
[2023-06-30 18:32:22,195] [INFO] Running command: blastn -query GCA_008671585.1_ASM867158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3da1836-1f79-41ea-af0d-5a47d82500b6/dqc_reference/reference_markers.fasta -out GCA_008671585.1_ASM867158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:32:22,814] [INFO] Task succeeded: Blastn
[2023-06-30 18:32:22,819] [INFO] Selected 22 target genomes.
[2023-06-30 18:32:22,819] [INFO] Target genome list was writen to GCA_008671585.1_ASM867158v1_genomic.fna/target_genomes.txt
[2023-06-30 18:32:22,822] [INFO] Task started: fastANI
[2023-06-30 18:32:22,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgae252e24-b022-4c9c-b72f-c4621c794950/GCA_008671585.1_ASM867158v1_genomic.fna.gz --refList GCA_008671585.1_ASM867158v1_genomic.fna/target_genomes.txt --output GCA_008671585.1_ASM867158v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:32:34,365] [INFO] Task succeeded: fastANI
[2023-06-30 18:32:34,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3da1836-1f79-41ea-af0d-5a47d82500b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:32:34,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3da1836-1f79-41ea-af0d-5a47d82500b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:32:34,370] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:32:34,370] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 18:32:34,370] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	80.1882	198	446	95	below_threshold
Ruminococcus bovis	strain=JE7A12	GCA_005601135.1	2564099	2564099	type	True	77.3448	73	446	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 18:32:34,373] [INFO] DFAST Taxonomy check result was written to GCA_008671585.1_ASM867158v1_genomic.fna/tc_result.tsv
[2023-06-30 18:32:34,373] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:32:34,374] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:32:34,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3da1836-1f79-41ea-af0d-5a47d82500b6/dqc_reference/checkm_data
[2023-06-30 18:32:34,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:32:34,401] [INFO] Task started: CheckM
[2023-06-30 18:32:34,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_008671585.1_ASM867158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_008671585.1_ASM867158v1_genomic.fna/checkm_input GCA_008671585.1_ASM867158v1_genomic.fna/checkm_result
[2023-06-30 18:32:52,134] [INFO] Task succeeded: CheckM
[2023-06-30 18:32:52,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:32:52,158] [INFO] ===== Completeness check finished =====
[2023-06-30 18:32:52,158] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:32:52,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_008671585.1_ASM867158v1_genomic.fna/markers.fasta)
[2023-06-30 18:32:52,159] [INFO] Task started: Blastn
[2023-06-30 18:32:52,159] [INFO] Running command: blastn -query GCA_008671585.1_ASM867158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3da1836-1f79-41ea-af0d-5a47d82500b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_008671585.1_ASM867158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:32:53,169] [INFO] Task succeeded: Blastn
[2023-06-30 18:32:53,174] [INFO] Selected 13 target genomes.
[2023-06-30 18:32:53,175] [INFO] Target genome list was writen to GCA_008671585.1_ASM867158v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:32:53,180] [INFO] Task started: fastANI
[2023-06-30 18:32:53,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgae252e24-b022-4c9c-b72f-c4621c794950/GCA_008671585.1_ASM867158v1_genomic.fna.gz --refList GCA_008671585.1_ASM867158v1_genomic.fna/target_genomes_gtdb.txt --output GCA_008671585.1_ASM867158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:32:58,234] [INFO] Task succeeded: fastANI
[2023-06-30 18:32:58,254] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 18:32:58,255] [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_014288065.1	s__Ruminococcus_E sp003526955	98.0505	387	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.97	97.37	0.85	0.74	16	conclusive
GCF_003438075.1	s__Ruminococcus_E sp003438075	90.5178	384	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.49	97.62	0.94	0.88	5	-
GCA_900755995.1	s__Ruminococcus_E sp900755995	82.4056	272	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834235.1	s__Ruminococcus_E bromii_B	81.1736	223	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.64	96.93	0.86	0.80	74	-
GCF_002834225.1	s__Ruminococcus_E bromii	80.1721	199	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.59	98.08	0.94	0.90	6	-
GCA_905215855.1	s__Ruminococcus_E sp905215855	80.0074	194	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.72	97.72	0.86	0.84	4	-
GCA_902766775.1	s__Ruminococcus_E sp902766775	79.4837	155	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003521625.1	s__Ruminococcus_E sp003521625	79.0098	143	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491825.1	s__Ruminococcus_E sp002491825	78.8569	118	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493635.1	s__Ruminococcus_E sp002493635	78.8464	124	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.92	97.46	0.88	0.85	4	-
GCA_902766885.1	s__Ruminococcus_E sp902766885	78.7658	155	446	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:32:58,258] [INFO] GTDB search result was written to GCA_008671585.1_ASM867158v1_genomic.fna/result_gtdb.tsv
[2023-06-30 18:32:58,258] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:32:58,262] [INFO] DFAST_QC result json was written to GCA_008671585.1_ASM867158v1_genomic.fna/dqc_result.json
[2023-06-30 18:32:58,262] [INFO] DFAST_QC completed!
[2023-06-30 18:32:58,262] [INFO] Total running time: 0h0m41s