[2024-01-25 20:18:35,818] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:35,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:35,820] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe24ef58-5070-4830-804c-e52cc00af5df/dqc_reference
[2024-01-25 20:18:37,003] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:37,004] [INFO] Task started: Prodigal
[2024-01-25 20:18:37,004] [INFO] Running command: gunzip -c /var/lib/cwl/stgacfc17d4-9ff3-41ee-9808-2aa521925c66/GCF_000007085.1_ASM708v1_genomic.fna.gz | prodigal -d GCF_000007085.1_ASM708v1_genomic.fna/cds.fna -a GCF_000007085.1_ASM708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:42,009] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:42,009] [INFO] Task started: HMMsearch
[2024-01-25 20:18:42,009] [INFO] Running command: hmmsearch --tblout GCF_000007085.1_ASM708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe24ef58-5070-4830-804c-e52cc00af5df/dqc_reference/reference_markers.hmm GCF_000007085.1_ASM708v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:42,233] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:42,234] [INFO] Found 6/6 markers.
[2024-01-25 20:18:42,258] [INFO] Query marker FASTA was written to GCF_000007085.1_ASM708v1_genomic.fna/markers.fasta
[2024-01-25 20:18:42,258] [INFO] Task started: Blastn
[2024-01-25 20:18:42,259] [INFO] Running command: blastn -query GCF_000007085.1_ASM708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe24ef58-5070-4830-804c-e52cc00af5df/dqc_reference/reference_markers.fasta -out GCF_000007085.1_ASM708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:42,783] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:42,787] [INFO] Selected 5 target genomes.
[2024-01-25 20:18:42,787] [INFO] Target genome list was writen to GCF_000007085.1_ASM708v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:42,792] [INFO] Task started: fastANI
[2024-01-25 20:18:42,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgacfc17d4-9ff3-41ee-9808-2aa521925c66/GCF_000007085.1_ASM708v1_genomic.fna.gz --refList GCF_000007085.1_ASM708v1_genomic.fna/target_genomes.txt --output GCF_000007085.1_ASM708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:47,876] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:47,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe24ef58-5070-4830-804c-e52cc00af5df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:47,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe24ef58-5070-4830-804c-e52cc00af5df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:47,882] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 20:18:47,883] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:47,883] [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
Caldanaerobacter subterraneus subsp. tengcongensis	strain=MB4	GCA_000007085.1	119072	911092	type	True	100.0	896	896	95	conclusive
Caldanaerobacter subterraneus subsp. tengcongensis	strain=MB4	GCA_024807135.1	119072	911092	type	True	99.9357	895	896	95	conclusive
Caldanaerobacter subterraneus subsp. pacificus	strain=DSM 12653	GCA_000156275.2	109807	911092	type	True	97.9074	619	896	95	conclusive
Caldanaerobacter subterraneus subsp. yonseiensis	strain=KB-1	GCA_000473865.1	111519	911092	type	True	97.8026	730	896	95	conclusive
Caldanaerobacter subterraneus	strain=DSM 13054	GCA_004345675.1	911092	911092	type	True	97.7458	690	896	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 20:18:47,884] [INFO] DFAST Taxonomy check result was written to GCF_000007085.1_ASM708v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:47,885] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:47,885] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:47,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe24ef58-5070-4830-804c-e52cc00af5df/dqc_reference/checkm_data
[2024-01-25 20:18:47,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:47,920] [INFO] Task started: CheckM
[2024-01-25 20:18:47,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000007085.1_ASM708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000007085.1_ASM708v1_genomic.fna/checkm_input GCF_000007085.1_ASM708v1_genomic.fna/checkm_result
[2024-01-25 20:19:08,571] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:08,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:08,601] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:08,601] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:08,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000007085.1_ASM708v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:08,602] [INFO] Task started: Blastn
[2024-01-25 20:19:08,602] [INFO] Running command: blastn -query GCF_000007085.1_ASM708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe24ef58-5070-4830-804c-e52cc00af5df/dqc_reference/reference_markers_gtdb.fasta -out GCF_000007085.1_ASM708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:09,351] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:09,355] [INFO] Selected 16 target genomes.
[2024-01-25 20:19:09,355] [INFO] Target genome list was writen to GCF_000007085.1_ASM708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:09,388] [INFO] Task started: fastANI
[2024-01-25 20:19:09,389] [INFO] Running command: fastANI --query /var/lib/cwl/stgacfc17d4-9ff3-41ee-9808-2aa521925c66/GCF_000007085.1_ASM708v1_genomic.fna.gz --refList GCF_000007085.1_ASM708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000007085.1_ASM708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:17,167] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:17,172] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:17,172] [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_004345675.1	s__Caldanaerobacter subterraneus	97.7458	690	896	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Caldanaerobacter	95.0	97.64	96.88	0.83	0.76	8	conclusive
GCA_014896455.1	s__Thermoanaerobacter sp014896455	84.0124	373	896	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.6271	N/A	N/A	N/A	N/A	1	-
GCA_003722315.1	s__Thermoanaerobacter ethanolicus	81.5119	377	896	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	96.9409	98.23	97.61	0.86	0.74	8	-
GCF_000147695.2	s__Thermoanaerobacter wiegelii	81.0314	377	896	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	96.9409	N/A	N/A	N/A	N/A	1	-
GCA_000445185.1	s__Thermoanaerobacter sp000445185	80.7398	323	896	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.9754	N/A	N/A	N/A	N/A	1	-
GCF_000019085.1	s__Thermoanaerobacter pseudethanolicus	80.6257	328	896	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.1128	98.35	97.55	0.89	0.81	10	-
GCF_900129115.1	s__Thermoanaerobacter uzonensis	80.2404	339	896	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.0	96.59	96.59	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:17,174] [INFO] GTDB search result was written to GCF_000007085.1_ASM708v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:17,174] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:17,176] [INFO] DFAST_QC result json was written to GCF_000007085.1_ASM708v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:17,177] [INFO] DFAST_QC completed!
[2024-01-25 20:19:17,177] [INFO] Total running time: 0h0m41s