[2024-01-24 12:51:05,487] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:05,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:05,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a48a333-5da5-4eef-90e7-6330e464c698/dqc_reference
[2024-01-24 12:51:06,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,696] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,697] [INFO] Running command: gunzip -c /var/lib/cwl/stge3920006-504d-4997-816c-b2265120d3b6/GCF_030014955.1_ASM3001495v1_genomic.fna.gz | prodigal -d GCF_030014955.1_ASM3001495v1_genomic.fna/cds.fna -a GCF_030014955.1_ASM3001495v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:31,620] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:31,621] [INFO] Task started: HMMsearch
[2024-01-24 12:51:31,621] [INFO] Running command: hmmsearch --tblout GCF_030014955.1_ASM3001495v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a48a333-5da5-4eef-90e7-6330e464c698/dqc_reference/reference_markers.hmm GCF_030014955.1_ASM3001495v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:31,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:31,991] [INFO] Found 6/6 markers.
[2024-01-24 12:51:32,060] [INFO] Query marker FASTA was written to GCF_030014955.1_ASM3001495v1_genomic.fna/markers.fasta
[2024-01-24 12:51:32,060] [INFO] Task started: Blastn
[2024-01-24 12:51:32,061] [INFO] Running command: blastn -query GCF_030014955.1_ASM3001495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a48a333-5da5-4eef-90e7-6330e464c698/dqc_reference/reference_markers.fasta -out GCF_030014955.1_ASM3001495v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:32,691] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:32,695] [INFO] Selected 14 target genomes.
[2024-01-24 12:51:32,695] [INFO] Target genome list was writen to GCF_030014955.1_ASM3001495v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:32,707] [INFO] Task started: fastANI
[2024-01-24 12:51:32,707] [INFO] Running command: fastANI --query /var/lib/cwl/stge3920006-504d-4997-816c-b2265120d3b6/GCF_030014955.1_ASM3001495v1_genomic.fna.gz --refList GCF_030014955.1_ASM3001495v1_genomic.fna/target_genomes.txt --output GCF_030014955.1_ASM3001495v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:49,033] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:49,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a48a333-5da5-4eef-90e7-6330e464c698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:49,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a48a333-5da5-4eef-90e7-6330e464c698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:49,050] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:51:49,051] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:51:49,051] [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 nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	79.2791	771	3019	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	78.7587	690	3019	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	78.6286	701	3019	95	below_threshold
Cohnella thailandensis	strain=DSM 25241	GCA_014212135.1	557557	557557	type	True	78.4123	597	3019	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	78.3043	406	3019	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	78.2768	409	3019	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	78.2679	486	3019	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	78.1924	649	3019	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.8508	443	3019	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.3803	495	3019	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.9586	199	3019	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.7937	192	3019	95	below_threshold
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	76.7197	219	3019	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.246	191	3019	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:49,052] [INFO] DFAST Taxonomy check result was written to GCF_030014955.1_ASM3001495v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:49,053] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:49,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:49,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a48a333-5da5-4eef-90e7-6330e464c698/dqc_reference/checkm_data
[2024-01-24 12:51:49,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:49,136] [INFO] Task started: CheckM
[2024-01-24 12:51:49,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030014955.1_ASM3001495v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030014955.1_ASM3001495v1_genomic.fna/checkm_input GCF_030014955.1_ASM3001495v1_genomic.fna/checkm_result
[2024-01-24 12:52:58,177] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:58,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:58,204] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:58,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:58,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030014955.1_ASM3001495v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:58,205] [INFO] Task started: Blastn
[2024-01-24 12:52:58,205] [INFO] Running command: blastn -query GCF_030014955.1_ASM3001495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a48a333-5da5-4eef-90e7-6330e464c698/dqc_reference/reference_markers_gtdb.fasta -out GCF_030014955.1_ASM3001495v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:59,062] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:59,066] [INFO] Selected 9 target genomes.
[2024-01-24 12:52:59,067] [INFO] Target genome list was writen to GCF_030014955.1_ASM3001495v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:59,090] [INFO] Task started: fastANI
[2024-01-24 12:52:59,090] [INFO] Running command: fastANI --query /var/lib/cwl/stge3920006-504d-4997-816c-b2265120d3b6/GCF_030014955.1_ASM3001495v1_genomic.fna.gz --refList GCF_030014955.1_ASM3001495v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030014955.1_ASM3001495v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:11,441] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:11,455] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:53:11,455] [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_003208555.1	s__Cohnella sp003208555	88.7581	1934	3019	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_019091135.1	s__Cohnella sp019091135	88.0072	1934	3019	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212125.1	s__Cohnella nanjingensis	79.2596	774	3019	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	78.7648	689	3019	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	78.6317	702	3019	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	78.2605	487	3019	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	78.2518	411	3019	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014212055.1	s__Cohnella zeiphila	78.1984	648	3019	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016937515.1	s__Cohnella algarum	78.0937	469	3019	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.08	99.08	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:11,457] [INFO] GTDB search result was written to GCF_030014955.1_ASM3001495v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:11,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:11,461] [INFO] DFAST_QC result json was written to GCF_030014955.1_ASM3001495v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:11,461] [INFO] DFAST_QC completed!
[2024-01-24 12:53:11,461] [INFO] Total running time: 0h2m6s