[2024-01-24 13:40:00,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:00,228] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:00,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg3656c98b-49e2-495f-85df-f995acf31321/dqc_reference
[2024-01-24 13:40:01,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:01,430] [INFO] Task started: Prodigal
[2024-01-24 13:40:01,430] [INFO] Running command: gunzip -c /var/lib/cwl/stg41d3e2aa-c0fb-434d-a492-e52bdef06ff4/GCF_005049045.1_ASM504904v1_genomic.fna.gz | prodigal -d GCF_005049045.1_ASM504904v1_genomic.fna/cds.fna -a GCF_005049045.1_ASM504904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:14,150] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:14,151] [INFO] Task started: HMMsearch
[2024-01-24 13:40:14,151] [INFO] Running command: hmmsearch --tblout GCF_005049045.1_ASM504904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3656c98b-49e2-495f-85df-f995acf31321/dqc_reference/reference_markers.hmm GCF_005049045.1_ASM504904v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:14,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:14,431] [INFO] Found 6/6 markers.
[2024-01-24 13:40:14,473] [INFO] Query marker FASTA was written to GCF_005049045.1_ASM504904v1_genomic.fna/markers.fasta
[2024-01-24 13:40:14,474] [INFO] Task started: Blastn
[2024-01-24 13:40:14,474] [INFO] Running command: blastn -query GCF_005049045.1_ASM504904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3656c98b-49e2-495f-85df-f995acf31321/dqc_reference/reference_markers.fasta -out GCF_005049045.1_ASM504904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:15,121] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:15,125] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:15,125] [INFO] Target genome list was writen to GCF_005049045.1_ASM504904v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:15,131] [INFO] Task started: fastANI
[2024-01-24 13:40:15,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg41d3e2aa-c0fb-434d-a492-e52bdef06ff4/GCF_005049045.1_ASM504904v1_genomic.fna.gz --refList GCF_005049045.1_ASM504904v1_genomic.fna/target_genomes.txt --output GCF_005049045.1_ASM504904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:30,859] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:30,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3656c98b-49e2-495f-85df-f995acf31321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:30,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3656c98b-49e2-495f-85df-f995acf31321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:30,879] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:30,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:30,879] [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 pontilimi	strain=CAU 1483	GCA_005049045.1	2564100	2564100	type	True	100.0	1416	1418	95	conclusive
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	79.1074	491	1418	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	78.1541	298	1418	95	below_threshold
Cohnella panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	77.9043	252	1418	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	77.8221	299	1418	95	below_threshold
Cohnella faecalis	strain=K2E09-144	GCA_003570905.1	2315694	2315694	type	True	77.8097	275	1418	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	77.627	287	1418	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	77.5493	224	1418	95	below_threshold
Cohnella luojiensis	strain=CCTCC AB 208254	GCA_004564235.1	652876	652876	type	True	77.5031	195	1418	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	77.487	228	1418	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	77.3747	216	1418	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	77.2814	214	1418	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.9438	137	1418	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.5815	122	1418	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.5719	68	1418	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.5622	131	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:30,881] [INFO] DFAST Taxonomy check result was written to GCF_005049045.1_ASM504904v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:30,882] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:30,882] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:30,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3656c98b-49e2-495f-85df-f995acf31321/dqc_reference/checkm_data
[2024-01-24 13:40:30,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:30,927] [INFO] Task started: CheckM
[2024-01-24 13:40:30,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005049045.1_ASM504904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005049045.1_ASM504904v1_genomic.fna/checkm_input GCF_005049045.1_ASM504904v1_genomic.fna/checkm_result
[2024-01-24 13:41:12,137] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:12,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:12,158] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:12,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:12,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005049045.1_ASM504904v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:12,160] [INFO] Task started: Blastn
[2024-01-24 13:41:12,160] [INFO] Running command: blastn -query GCF_005049045.1_ASM504904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3656c98b-49e2-495f-85df-f995acf31321/dqc_reference/reference_markers_gtdb.fasta -out GCF_005049045.1_ASM504904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:13,079] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:13,083] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:13,084] [INFO] Target genome list was writen to GCF_005049045.1_ASM504904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:13,107] [INFO] Task started: fastANI
[2024-01-24 13:41:13,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg41d3e2aa-c0fb-434d-a492-e52bdef06ff4/GCF_005049045.1_ASM504904v1_genomic.fna.gz --refList GCF_005049045.1_ASM504904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005049045.1_ASM504904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:29,495] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:29,507] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:29,507] [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_005049045.1	s__Cohnella pontilimi	100.0	1416	1418	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_003713065.1	s__Cohnella candidum	79.1074	491	1418	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429825.1	s__Cohnella thermotolerans	78.1594	296	1418	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	77.8812	260	1418	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.08	99.08	0.87	0.87	3	-
GCF_000515335.1	s__Cohnella panacarvi	77.8772	254	1418	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	77.8109	300	1418	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570905.1	s__Cohnella faecalis	77.7977	276	1418	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	77.7207	271	1418	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001675.1	s__Cohnella sp003001675	77.6496	313	1418	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014212055.1	s__Cohnella zeiphila	77.6265	287	1418	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	77.5852	303	1418	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_014212015.1	s__Cohnella lubricantis	77.5497	224	1418	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004801405.1	s__Cohnella sp004801405	77.3747	216	1418	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 13:41:29,510] [INFO] GTDB search result was written to GCF_005049045.1_ASM504904v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:29,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:29,518] [INFO] DFAST_QC result json was written to GCF_005049045.1_ASM504904v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:29,519] [INFO] DFAST_QC completed!
[2024-01-24 13:41:29,519] [INFO] Total running time: 0h1m29s