[2024-01-24 14:12:03,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:03,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:03,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg4976e512-0e42-4da4-ab22-1a1eeaa2e202/dqc_reference
[2024-01-24 14:12:05,404] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:05,405] [INFO] Task started: Prodigal
[2024-01-24 14:12:05,405] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c76a2b0-4dbf-4641-949c-c869053f473a/GCF_004564235.1_ASM456423v1_genomic.fna.gz | prodigal -d GCF_004564235.1_ASM456423v1_genomic.fna/cds.fna -a GCF_004564235.1_ASM456423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:19,247] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:19,248] [INFO] Task started: HMMsearch
[2024-01-24 14:12:19,248] [INFO] Running command: hmmsearch --tblout GCF_004564235.1_ASM456423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4976e512-0e42-4da4-ab22-1a1eeaa2e202/dqc_reference/reference_markers.hmm GCF_004564235.1_ASM456423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:19,597] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:19,598] [INFO] Found 6/6 markers.
[2024-01-24 14:12:19,643] [INFO] Query marker FASTA was written to GCF_004564235.1_ASM456423v1_genomic.fna/markers.fasta
[2024-01-24 14:12:19,644] [INFO] Task started: Blastn
[2024-01-24 14:12:19,644] [INFO] Running command: blastn -query GCF_004564235.1_ASM456423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4976e512-0e42-4da4-ab22-1a1eeaa2e202/dqc_reference/reference_markers.fasta -out GCF_004564235.1_ASM456423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:20,286] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:20,289] [INFO] Selected 12 target genomes.
[2024-01-24 14:12:20,290] [INFO] Target genome list was writen to GCF_004564235.1_ASM456423v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:20,295] [INFO] Task started: fastANI
[2024-01-24 14:12:20,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c76a2b0-4dbf-4641-949c-c869053f473a/GCF_004564235.1_ASM456423v1_genomic.fna.gz --refList GCF_004564235.1_ASM456423v1_genomic.fna/target_genomes.txt --output GCF_004564235.1_ASM456423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:36,705] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:36,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4976e512-0e42-4da4-ab22-1a1eeaa2e202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:36,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4976e512-0e42-4da4-ab22-1a1eeaa2e202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:36,716] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:36,716] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:36,716] [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
Cohnella luojiensis	strain=CCTCC AB 208254	GCA_004564235.1	652876	652876	type	True	100.0	1631	1635	95	conclusive
Cohnella lupini	strain=CECT 8236	GCA_003386205.1	1294267	1294267	type	True	80.9463	791	1635	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	80.0876	659	1635	95	below_threshold
Cohnella cholangitidis	strain=1605-214	GCA_014107495.1	2598458	2598458	type	True	80.0159	626	1635	95	below_threshold
Cohnella endophytica	strain=M2MS4P-1	GCA_003628305.1	2419778	2419778	type	True	79.7702	567	1635	95	below_threshold
Cohnella abietis	strain=HS21	GCA_004295585.1	2507935	2507935	type	True	79.2218	432	1635	95	below_threshold
Cohnella terricola	strain=G13	GCA_007786475.1	1289167	1289167	type	True	79.0817	419	1635	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	77.0335	176	1635	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.8418	176	1635	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.3414	102	1635	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.2849	76	1635	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:36,720] [INFO] DFAST Taxonomy check result was written to GCF_004564235.1_ASM456423v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:36,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:36,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:36,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4976e512-0e42-4da4-ab22-1a1eeaa2e202/dqc_reference/checkm_data
[2024-01-24 14:12:36,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:36,771] [INFO] Task started: CheckM
[2024-01-24 14:12:36,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004564235.1_ASM456423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004564235.1_ASM456423v1_genomic.fna/checkm_input GCF_004564235.1_ASM456423v1_genomic.fna/checkm_result
[2024-01-24 14:13:17,569] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:17,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:17,586] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:17,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:17,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004564235.1_ASM456423v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:17,587] [INFO] Task started: Blastn
[2024-01-24 14:13:17,588] [INFO] Running command: blastn -query GCF_004564235.1_ASM456423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4976e512-0e42-4da4-ab22-1a1eeaa2e202/dqc_reference/reference_markers_gtdb.fasta -out GCF_004564235.1_ASM456423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:18,392] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:18,397] [INFO] Selected 9 target genomes.
[2024-01-24 14:13:18,397] [INFO] Target genome list was writen to GCF_004564235.1_ASM456423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:18,407] [INFO] Task started: fastANI
[2024-01-24 14:13:18,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c76a2b0-4dbf-4641-949c-c869053f473a/GCF_004564235.1_ASM456423v1_genomic.fna.gz --refList GCF_004564235.1_ASM456423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004564235.1_ASM456423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:28,597] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:28,608] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:28,608] [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_004564235.1	s__Cohnella luojiensis	100.0	1631	1635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003386205.1	s__Cohnella lupini	80.9409	791	1635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849095.1	s__Cohnella sp012849095	80.096	658	1635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014107495.1	s__Cohnella sp014107495	80.0159	626	1635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628305.1	s__Cohnella endophytica	79.7812	567	1635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295585.1	s__Cohnella abietis	79.2275	431	1635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874175.1	s__Cohnella suwonensis	79.2011	479	1635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908615.1	s__Cohnella boryungensis	78.6344	404	1635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212015.1	s__Cohnella lubricantis	77.0535	173	1635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:28,610] [INFO] GTDB search result was written to GCF_004564235.1_ASM456423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:28,610] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:28,616] [INFO] DFAST_QC result json was written to GCF_004564235.1_ASM456423v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:28,616] [INFO] DFAST_QC completed!
[2024-01-24 14:13:28,616] [INFO] Total running time: 0h1m25s