[2024-01-25 19:53:35,581] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:35,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:35,583] [INFO] DQC Reference Directory: /var/lib/cwl/stgf70d974e-2e4f-4b53-9355-fe7b92b45385/dqc_reference
[2024-01-25 19:53:36,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:36,721] [INFO] Task started: Prodigal
[2024-01-25 19:53:36,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg929e70b9-257a-4f07-9504-a953114df84d/GCF_014646935.1_ASM1464693v1_genomic.fna.gz | prodigal -d GCF_014646935.1_ASM1464693v1_genomic.fna/cds.fna -a GCF_014646935.1_ASM1464693v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:43,179] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:43,179] [INFO] Task started: HMMsearch
[2024-01-25 19:53:43,179] [INFO] Running command: hmmsearch --tblout GCF_014646935.1_ASM1464693v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf70d974e-2e4f-4b53-9355-fe7b92b45385/dqc_reference/reference_markers.hmm GCF_014646935.1_ASM1464693v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:43,353] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:43,355] [INFO] Found 6/6 markers.
[2024-01-25 19:53:43,377] [INFO] Query marker FASTA was written to GCF_014646935.1_ASM1464693v1_genomic.fna/markers.fasta
[2024-01-25 19:53:43,377] [INFO] Task started: Blastn
[2024-01-25 19:53:43,377] [INFO] Running command: blastn -query GCF_014646935.1_ASM1464693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf70d974e-2e4f-4b53-9355-fe7b92b45385/dqc_reference/reference_markers.fasta -out GCF_014646935.1_ASM1464693v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:43,974] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:43,987] [INFO] Selected 14 target genomes.
[2024-01-25 19:53:43,988] [INFO] Target genome list was writen to GCF_014646935.1_ASM1464693v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:43,996] [INFO] Task started: fastANI
[2024-01-25 19:53:43,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg929e70b9-257a-4f07-9504-a953114df84d/GCF_014646935.1_ASM1464693v1_genomic.fna.gz --refList GCF_014646935.1_ASM1464693v1_genomic.fna/target_genomes.txt --output GCF_014646935.1_ASM1464693v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:52,924] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:52,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf70d974e-2e4f-4b53-9355-fe7b92b45385/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:52,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf70d974e-2e4f-4b53-9355-fe7b92b45385/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:52,932] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:53:52,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:53:52,932] [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
Calditerricola satsumensis	strain=JCM 14719	GCA_014646935.1	373054	373054	type	True	100.0	742	745	95	conclusive
Calditerricola satsumensis	strain=JCM 14719	GCA_001311905.1	373054	373054	type	True	99.2576	442	745	95	conclusive
Planifilum fimeticola	strain=DSM 44946	GCA_003001905.1	201975	201975	type	True	76.644	70	745	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	76.5966	83	745	95	below_threshold
Paenibacillus pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	76.5726	84	745	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	76.0201	76	745	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	75.8982	53	745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:52,933] [INFO] DFAST Taxonomy check result was written to GCF_014646935.1_ASM1464693v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:52,935] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:52,936] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:52,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf70d974e-2e4f-4b53-9355-fe7b92b45385/dqc_reference/checkm_data
[2024-01-25 19:53:52,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:52,980] [INFO] Task started: CheckM
[2024-01-25 19:53:52,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646935.1_ASM1464693v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646935.1_ASM1464693v1_genomic.fna/checkm_input GCF_014646935.1_ASM1464693v1_genomic.fna/checkm_result
[2024-01-25 19:54:17,012] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:17,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:17,029] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:17,029] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:17,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646935.1_ASM1464693v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:17,030] [INFO] Task started: Blastn
[2024-01-25 19:54:17,030] [INFO] Running command: blastn -query GCF_014646935.1_ASM1464693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf70d974e-2e4f-4b53-9355-fe7b92b45385/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646935.1_ASM1464693v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:17,951] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:17,953] [INFO] Selected 16 target genomes.
[2024-01-25 19:54:17,954] [INFO] Target genome list was writen to GCF_014646935.1_ASM1464693v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:17,969] [INFO] Task started: fastANI
[2024-01-25 19:54:17,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg929e70b9-257a-4f07-9504-a953114df84d/GCF_014646935.1_ASM1464693v1_genomic.fna.gz --refList GCF_014646935.1_ASM1464693v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646935.1_ASM1464693v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:29,170] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:29,178] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:29,178] [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_014646935.1	s__Calditerricola satsumensis	100.0	742	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Calditerricolales;f__Calditerricolaceae;g__Calditerricola	95.0	99.92	99.92	0.99	0.99	2	conclusive
GCA_017577925.1	s__Calditerricola sp017577925	87.7289	431	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Calditerricolales;f__Calditerricolaceae;g__Calditerricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001905.1	s__Planifilum fimeticola	76.6733	69	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422485.1	s__Paenibacillus_O pasadenensis	76.5966	83	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.23	98.68	0.94	0.90	4	-
GCF_000454065.1	s__Brevibacillus thermoruber	76.5944	118	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.54	98.43	0.91	0.89	5	-
GCA_002159085.1	s__Thermobacillus sp002159085	76.5293	95	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208555.1	s__Cohnella sp003208555	76.1074	56	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004340785.1	s__Tumebacillus_A sp004340785	76.0518	55	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212175.1	s__Cohnella xylanilytica	76.0201	76	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_018403265.1	s__J31TS4 sp018403265	76.0161	51	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__J31TS4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212055.1	s__Cohnella zeiphila	75.8982	53	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:29,179] [INFO] GTDB search result was written to GCF_014646935.1_ASM1464693v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:29,180] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:29,185] [INFO] DFAST_QC result json was written to GCF_014646935.1_ASM1464693v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:29,186] [INFO] DFAST_QC completed!
[2024-01-25 19:54:29,186] [INFO] Total running time: 0h0m54s