[2024-01-25 19:50:05,516] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:05,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:05,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgc427d0d7-8c4e-4783-8a37-c7c3518ca78d/dqc_reference
[2024-01-25 19:50:06,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:06,687] [INFO] Task started: Prodigal
[2024-01-25 19:50:06,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg36e10ea9-275e-4009-a64b-65168be50d5f/GCF_003865095.1_ASM386509v1_genomic.fna.gz | prodigal -d GCF_003865095.1_ASM386509v1_genomic.fna/cds.fna -a GCF_003865095.1_ASM386509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:14,060] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:14,060] [INFO] Task started: HMMsearch
[2024-01-25 19:50:14,060] [INFO] Running command: hmmsearch --tblout GCF_003865095.1_ASM386509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc427d0d7-8c4e-4783-8a37-c7c3518ca78d/dqc_reference/reference_markers.hmm GCF_003865095.1_ASM386509v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:14,337] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:14,338] [INFO] Found 6/6 markers.
[2024-01-25 19:50:14,381] [INFO] Query marker FASTA was written to GCF_003865095.1_ASM386509v1_genomic.fna/markers.fasta
[2024-01-25 19:50:14,382] [INFO] Task started: Blastn
[2024-01-25 19:50:14,382] [INFO] Running command: blastn -query GCF_003865095.1_ASM386509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc427d0d7-8c4e-4783-8a37-c7c3518ca78d/dqc_reference/reference_markers.fasta -out GCF_003865095.1_ASM386509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:14,937] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:14,943] [INFO] Selected 13 target genomes.
[2024-01-25 19:50:14,943] [INFO] Target genome list was writen to GCF_003865095.1_ASM386509v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:14,961] [INFO] Task started: fastANI
[2024-01-25 19:50:14,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg36e10ea9-275e-4009-a64b-65168be50d5f/GCF_003865095.1_ASM386509v1_genomic.fna.gz --refList GCF_003865095.1_ASM386509v1_genomic.fna/target_genomes.txt --output GCF_003865095.1_ASM386509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:26,856] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:26,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc427d0d7-8c4e-4783-8a37-c7c3518ca78d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:26,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc427d0d7-8c4e-4783-8a37-c7c3518ca78d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:26,864] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:50:26,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:26,864] [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
Clostridium tagluense	strain=A121	GCA_003865095.1	360422	360422	type	True	100.0	1663	1667	95	conclusive
Clostridium bowmanii	strain=DSM 14206	GCA_018861315.1	132925	132925	type	True	84.4687	959	1667	95	below_threshold
Clostridium bowmanii	strain=DSM 14206	GCA_020176155.1	132925	132925	type	True	84.4436	943	1667	95	below_threshold
Clostridium algoriphilum	strain=DSM 16153	GCA_020443705.1	198347	198347	type	True	81.8438	681	1667	95	below_threshold
Clostridium frigoris	strain=DSM 14204	GCA_018861865.1	205327	205327	type	True	81.3105	675	1667	95	below_threshold
Clostridium estertheticum subsp. estertheticum	strain=DSM 8809	GCA_001877035.1	1552	238834	type	True	81.2668	706	1667	95	below_threshold
Clostridium lacusfryxellense	strain=DSM 14205	GCA_018861735.1	205328	205328	type	True	80.9859	727	1667	95	below_threshold
Clostridium psychrophilum	strain=DSM 14207	GCA_018861705.1	132926	132926	type	True	80.645	613	1667	95	below_threshold
Clostridium grantii	strain=DSM 8605	GCA_900129965.1	40575	40575	type	True	76.19	141	1667	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	75.9342	109	1667	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	75.7229	125	1667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:26,866] [INFO] DFAST Taxonomy check result was written to GCF_003865095.1_ASM386509v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:26,866] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:26,866] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:26,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc427d0d7-8c4e-4783-8a37-c7c3518ca78d/dqc_reference/checkm_data
[2024-01-25 19:50:26,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:26,919] [INFO] Task started: CheckM
[2024-01-25 19:50:26,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003865095.1_ASM386509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003865095.1_ASM386509v1_genomic.fna/checkm_input GCF_003865095.1_ASM386509v1_genomic.fna/checkm_result
[2024-01-25 19:50:53,867] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:53,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:53,887] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:53,887] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:53,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003865095.1_ASM386509v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:53,887] [INFO] Task started: Blastn
[2024-01-25 19:50:53,887] [INFO] Running command: blastn -query GCF_003865095.1_ASM386509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc427d0d7-8c4e-4783-8a37-c7c3518ca78d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003865095.1_ASM386509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:54,657] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:54,660] [INFO] Selected 7 target genomes.
[2024-01-25 19:50:54,660] [INFO] Target genome list was writen to GCF_003865095.1_ASM386509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:54,667] [INFO] Task started: fastANI
[2024-01-25 19:50:54,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg36e10ea9-275e-4009-a64b-65168be50d5f/GCF_003865095.1_ASM386509v1_genomic.fna.gz --refList GCF_003865095.1_ASM386509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003865095.1_ASM386509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:03,135] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:03,140] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:03,141] [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_003865095.1	s__Clostridium_AD tagluense	100.0	1663	1667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	96.49	95.92	0.80	0.78	4	conclusive
GCF_011065935.1	s__Clostridium_AD estertheticum_A	87.8093	1082	1667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861755.1	s__Clostridium_AD sp018861755	87.7918	1116	1667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861315.1	s__Clostridium_AD bowmanii	84.46	960	1667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011065905.1	s__Clostridium_AD estertheticum_B	84.0209	761	1667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	97.19	97.19	0.83	0.83	2	-
GCA_016650095.1	s__Clostridium_AD sp016650095	83.5067	595	1667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650035.1	s__Clostridium_AD sp016650035	81.9259	672	1667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:03,142] [INFO] GTDB search result was written to GCF_003865095.1_ASM386509v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:03,142] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:03,145] [INFO] DFAST_QC result json was written to GCF_003865095.1_ASM386509v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:03,145] [INFO] DFAST_QC completed!
[2024-01-25 19:51:03,145] [INFO] Total running time: 0h0m58s