[2024-01-24 15:18:51,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,978] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,978] [INFO] DQC Reference Directory: /var/lib/cwl/stgd01fd3c2-c5ed-4797-8df4-64dfe33a9ec6/dqc_reference
[2024-01-24 15:18:54,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:54,593] [INFO] Task started: Prodigal
[2024-01-24 15:18:54,594] [INFO] Running command: gunzip -c /var/lib/cwl/stgd64ec44b-ef11-4e2d-8fdb-d9998cb289a4/GCF_017874075.1_ASM1787407v1_genomic.fna.gz | prodigal -d GCF_017874075.1_ASM1787407v1_genomic.fna/cds.fna -a GCF_017874075.1_ASM1787407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:12,807] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:12,807] [INFO] Task started: HMMsearch
[2024-01-24 15:19:12,807] [INFO] Running command: hmmsearch --tblout GCF_017874075.1_ASM1787407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd01fd3c2-c5ed-4797-8df4-64dfe33a9ec6/dqc_reference/reference_markers.hmm GCF_017874075.1_ASM1787407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:13,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:13,213] [INFO] Found 6/6 markers.
[2024-01-24 15:19:13,270] [INFO] Query marker FASTA was written to GCF_017874075.1_ASM1787407v1_genomic.fna/markers.fasta
[2024-01-24 15:19:13,271] [INFO] Task started: Blastn
[2024-01-24 15:19:13,271] [INFO] Running command: blastn -query GCF_017874075.1_ASM1787407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd01fd3c2-c5ed-4797-8df4-64dfe33a9ec6/dqc_reference/reference_markers.fasta -out GCF_017874075.1_ASM1787407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:13,915] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:13,918] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:13,918] [INFO] Target genome list was writen to GCF_017874075.1_ASM1787407v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:13,926] [INFO] Task started: fastANI
[2024-01-24 15:19:13,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgd64ec44b-ef11-4e2d-8fdb-d9998cb289a4/GCF_017874075.1_ASM1787407v1_genomic.fna.gz --refList GCF_017874075.1_ASM1787407v1_genomic.fna/target_genomes.txt --output GCF_017874075.1_ASM1787407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:30,037] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:30,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd01fd3c2-c5ed-4797-8df4-64dfe33a9ec6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:30,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd01fd3c2-c5ed-4797-8df4-64dfe33a9ec6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:30,049] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:30,049] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:30,049] [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 thailandensis	strain=DSM 25241	GCA_017874075.1	557557	557557	type	True	100.0	2291	2291	95	conclusive
Cohnella thailandensis	strain=DSM 25241	GCA_014212135.1	557557	557557	type	True	99.9901	2277	2291	95	conclusive
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	82.6542	1196	2291	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	80.5943	929	2291	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	79.4109	630	2291	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	79.2824	702	2291	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	79.2077	565	2291	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	79.1652	560	2291	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.5379	422	2291	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.0756	213	2291	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.9756	105	2291	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	76.509	70	2291	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.4072	119	2291	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:30,051] [INFO] DFAST Taxonomy check result was written to GCF_017874075.1_ASM1787407v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:30,052] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:30,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:30,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd01fd3c2-c5ed-4797-8df4-64dfe33a9ec6/dqc_reference/checkm_data
[2024-01-24 15:19:30,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:30,119] [INFO] Task started: CheckM
[2024-01-24 15:19:30,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874075.1_ASM1787407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874075.1_ASM1787407v1_genomic.fna/checkm_input GCF_017874075.1_ASM1787407v1_genomic.fna/checkm_result
[2024-01-24 15:20:21,045] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:21,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:21,069] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:21,070] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:21,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874075.1_ASM1787407v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:21,071] [INFO] Task started: Blastn
[2024-01-24 15:20:21,071] [INFO] Running command: blastn -query GCF_017874075.1_ASM1787407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd01fd3c2-c5ed-4797-8df4-64dfe33a9ec6/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874075.1_ASM1787407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:22,026] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:22,029] [INFO] Selected 8 target genomes.
[2024-01-24 15:20:22,030] [INFO] Target genome list was writen to GCF_017874075.1_ASM1787407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:22,035] [INFO] Task started: fastANI
[2024-01-24 15:20:22,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgd64ec44b-ef11-4e2d-8fdb-d9998cb289a4/GCF_017874075.1_ASM1787407v1_genomic.fna.gz --refList GCF_017874075.1_ASM1787407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874075.1_ASM1787407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:33,246] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:33,259] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:33,259] [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_014212135.1	s__Cohnella thailandensis	99.9901	2277	2291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003990975.1	s__Cohnella sp003990975	82.677	1134	2291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801405.1	s__Cohnella sp004801405	82.6508	1197	2291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212175.1	s__Cohnella xylanilytica	80.5928	930	2291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_000429825.1	s__Cohnella thermotolerans	79.4269	627	2291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212055.1	s__Cohnella zeiphila	79.3106	699	2291	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	79.1561	562	2291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014212125.1	s__Cohnella nanjingensis	78.7765	652	2291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:33,260] [INFO] GTDB search result was written to GCF_017874075.1_ASM1787407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:33,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:33,264] [INFO] DFAST_QC result json was written to GCF_017874075.1_ASM1787407v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:33,264] [INFO] DFAST_QC completed!
[2024-01-24 15:20:33,264] [INFO] Total running time: 0h1m41s