[2024-01-24 15:02:24,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,068] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,068] [INFO] DQC Reference Directory: /var/lib/cwl/stgf77e5fcb-0640-4958-a9d7-6d73beaf1873/dqc_reference
[2024-01-24 15:02:26,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,428] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,428] [INFO] Running command: gunzip -c /var/lib/cwl/stgd833696a-400a-42f3-b76a-18636250375b/GCF_005601135.1_ASM560113v1_genomic.fna.gz | prodigal -d GCF_005601135.1_ASM560113v1_genomic.fna/cds.fna -a GCF_005601135.1_ASM560113v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:31,546] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:31,547] [INFO] Task started: HMMsearch
[2024-01-24 15:02:31,548] [INFO] Running command: hmmsearch --tblout GCF_005601135.1_ASM560113v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf77e5fcb-0640-4958-a9d7-6d73beaf1873/dqc_reference/reference_markers.hmm GCF_005601135.1_ASM560113v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:31,808] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:31,810] [INFO] Found 6/6 markers.
[2024-01-24 15:02:31,840] [INFO] Query marker FASTA was written to GCF_005601135.1_ASM560113v1_genomic.fna/markers.fasta
[2024-01-24 15:02:31,840] [INFO] Task started: Blastn
[2024-01-24 15:02:31,840] [INFO] Running command: blastn -query GCF_005601135.1_ASM560113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf77e5fcb-0640-4958-a9d7-6d73beaf1873/dqc_reference/reference_markers.fasta -out GCF_005601135.1_ASM560113v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:32,766] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:32,769] [INFO] Selected 20 target genomes.
[2024-01-24 15:02:32,770] [INFO] Target genome list was writen to GCF_005601135.1_ASM560113v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:32,821] [INFO] Task started: fastANI
[2024-01-24 15:02:32,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgd833696a-400a-42f3-b76a-18636250375b/GCF_005601135.1_ASM560113v1_genomic.fna.gz --refList GCF_005601135.1_ASM560113v1_genomic.fna/target_genomes.txt --output GCF_005601135.1_ASM560113v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:44,484] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:44,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf77e5fcb-0640-4958-a9d7-6d73beaf1873/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:44,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf77e5fcb-0640-4958-a9d7-6d73beaf1873/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:44,489] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:44,489] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:44,489] [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 bovis	strain=JE7A12	GCA_005601135.1	2564099	2564099	type	True	100.0	813	813	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 15:02:44,491] [INFO] DFAST Taxonomy check result was written to GCF_005601135.1_ASM560113v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:44,491] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:44,491] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:44,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf77e5fcb-0640-4958-a9d7-6d73beaf1873/dqc_reference/checkm_data
[2024-01-24 15:02:44,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:44,525] [INFO] Task started: CheckM
[2024-01-24 15:02:44,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005601135.1_ASM560113v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005601135.1_ASM560113v1_genomic.fna/checkm_input GCF_005601135.1_ASM560113v1_genomic.fna/checkm_result
[2024-01-24 15:03:07,651] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:07,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:07,685] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:07,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:07,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005601135.1_ASM560113v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:07,686] [INFO] Task started: Blastn
[2024-01-24 15:03:07,686] [INFO] Running command: blastn -query GCF_005601135.1_ASM560113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf77e5fcb-0640-4958-a9d7-6d73beaf1873/dqc_reference/reference_markers_gtdb.fasta -out GCF_005601135.1_ASM560113v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:08,744] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:08,749] [INFO] Selected 21 target genomes.
[2024-01-24 15:03:08,749] [INFO] Target genome list was writen to GCF_005601135.1_ASM560113v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:08,781] [INFO] Task started: fastANI
[2024-01-24 15:03:08,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgd833696a-400a-42f3-b76a-18636250375b/GCF_005601135.1_ASM560113v1_genomic.fna.gz --refList GCF_005601135.1_ASM560113v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005601135.1_ASM560113v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:17,777] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:17,787] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:17,787] [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_005601135.1	s__Ruminococcus_E sp900314705	100.0	813	813	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	96.56	95.43	0.90	0.83	11	conclusive
GCF_003438075.1	s__Ruminococcus_E sp003438075	78.1574	104	813	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	-
GCF_002834235.1	s__Ruminococcus_E bromii_B	78.0871	94	813	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	-
GCA_017458105.1	s__Ruminococcus_E sp017458105	77.4232	114	813	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_000435335.1	s__CAG-964 sp000435335	77.115	66	813	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-964	95.0	99.05	99.03	0.94	0.93	3	-
GCA_017410265.1	s__Ruminococcus_E sp017410265	77.1035	53	813	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.82	97.82	0.84	0.84	2	-
GCA_017481885.1	s__Ruminococcus_E sp017481885	76.9081	54	813	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_017473555.1	s__Ruminococcus_E sp017473555	76.8699	65	813	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_014288065.1	s__Ruminococcus_E sp003526955	76.869	108	813	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	-
GCA_902766885.1	s__Ruminococcus_E sp902766885	76.3453	51	813	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	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:17,793] [INFO] GTDB search result was written to GCF_005601135.1_ASM560113v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:17,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:17,797] [INFO] DFAST_QC result json was written to GCF_005601135.1_ASM560113v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:17,797] [INFO] DFAST_QC completed!
[2024-01-24 15:03:17,798] [INFO] Total running time: 0h0m54s