[2024-01-24 12:14:48,972] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,977] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d2a1491-9e91-444b-b5c2-20b070bce48f/dqc_reference
[2024-01-24 12:14:50,359] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,360] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,360] [INFO] Running command: gunzip -c /var/lib/cwl/stgf975cb5c-9959-47fa-a1a9-b7954bb52b8f/GCF_004916975.1_ASM491697v1_genomic.fna.gz | prodigal -d GCF_004916975.1_ASM491697v1_genomic.fna/cds.fna -a GCF_004916975.1_ASM491697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:08,439] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:08,440] [INFO] Task started: HMMsearch
[2024-01-24 12:15:08,440] [INFO] Running command: hmmsearch --tblout GCF_004916975.1_ASM491697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d2a1491-9e91-444b-b5c2-20b070bce48f/dqc_reference/reference_markers.hmm GCF_004916975.1_ASM491697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:08,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:08,877] [INFO] Found 6/6 markers.
[2024-01-24 12:15:08,937] [INFO] Query marker FASTA was written to GCF_004916975.1_ASM491697v1_genomic.fna/markers.fasta
[2024-01-24 12:15:08,938] [INFO] Task started: Blastn
[2024-01-24 12:15:08,938] [INFO] Running command: blastn -query GCF_004916975.1_ASM491697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2a1491-9e91-444b-b5c2-20b070bce48f/dqc_reference/reference_markers.fasta -out GCF_004916975.1_ASM491697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:09,564] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:09,569] [INFO] Selected 26 target genomes.
[2024-01-24 12:15:09,570] [INFO] Target genome list was writen to GCF_004916975.1_ASM491697v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:09,581] [INFO] Task started: fastANI
[2024-01-24 12:15:09,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgf975cb5c-9959-47fa-a1a9-b7954bb52b8f/GCF_004916975.1_ASM491697v1_genomic.fna.gz --refList GCF_004916975.1_ASM491697v1_genomic.fna/target_genomes.txt --output GCF_004916975.1_ASM491697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:36,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:36,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d2a1491-9e91-444b-b5c2-20b070bce48f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:36,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d2a1491-9e91-444b-b5c2-20b070bce48f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:36,542] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:36,542] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:36,542] [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
Paenibacillus dokdonensis	strain=YH-JAE5	GCA_004916975.1	2567944	2567944	type	True	100.0	2157	2157	95	conclusive
Paenibacillus chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	82.5048	1187	2157	95	below_threshold
Paenibacillus rhizosphaerae	strain=CECT 5831	GCA_014192015.1	297318	297318	type	True	79.0165	598	2157	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_001315125.1	669461	669461	type	True	78.5243	348	2157	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_000576305.1	669461	669461	type	True	78.5128	349	2157	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	78.4303	252	2157	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	78.3809	309	2157	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	77.7371	210	2157	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.71	205	2157	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.7038	201	2157	95	below_threshold
Paenibacillus macerans	strain=NCTC6355	GCA_900454495.1	44252	44252	type	True	77.6824	207	2157	95	below_threshold
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	77.6443	193	2157	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	77.6047	201	2157	95	below_threshold
Paenibacillus glucanolyticus	strain=NBRC 15330	GCA_004000885.1	59843	59843	type	True	77.5346	259	2157	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.5103	169	2157	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	77.5038	193	2157	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	77.3386	194	2157	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	77.3258	202	2157	95	below_threshold
Paenibacillus lactis	strain=DSM 15596	GCA_017873605.1	228574	228574	type	True	77.3021	278	2157	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	77.2136	195	2157	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	77.1455	101	2157	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.0677	170	2157	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.0088	157	2157	95	below_threshold
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	76.7288	103	2157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:36,543] [INFO] DFAST Taxonomy check result was written to GCF_004916975.1_ASM491697v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:36,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:36,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:36,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d2a1491-9e91-444b-b5c2-20b070bce48f/dqc_reference/checkm_data
[2024-01-24 12:15:36,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:36,609] [INFO] Task started: CheckM
[2024-01-24 12:15:36,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004916975.1_ASM491697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004916975.1_ASM491697v1_genomic.fna/checkm_input GCF_004916975.1_ASM491697v1_genomic.fna/checkm_result
[2024-01-24 12:16:30,242] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:30,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:30,272] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:30,272] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:30,273] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004916975.1_ASM491697v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:30,273] [INFO] Task started: Blastn
[2024-01-24 12:16:30,273] [INFO] Running command: blastn -query GCF_004916975.1_ASM491697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2a1491-9e91-444b-b5c2-20b070bce48f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004916975.1_ASM491697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:31,073] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:31,076] [INFO] Selected 11 target genomes.
[2024-01-24 12:16:31,077] [INFO] Target genome list was writen to GCF_004916975.1_ASM491697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:31,085] [INFO] Task started: fastANI
[2024-01-24 12:16:31,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgf975cb5c-9959-47fa-a1a9-b7954bb52b8f/GCF_004916975.1_ASM491697v1_genomic.fna.gz --refList GCF_004916975.1_ASM491697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004916975.1_ASM491697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:45,070] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:45,085] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:45,085] [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_004916975.1	s__Paenibacillus dokdonensis	100.0	2157	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018403225.1	s__Paenibacillus sp018403225	94.9514	1844	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807035.1	s__Paenibacillus sp009807035	83.2364	1403	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001045.1	s__Paenibacillus chibensis	82.5205	1184	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333315.1	s__Paenibacillus azoreducens	80.6256	1001	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.74	97.74	0.88	0.88	2	-
GCF_009870825.1	s__Paenibacillus albilobatus	80.2683	888	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.80	99.80	0.98	0.98	2	-
GCF_018333375.1	s__Paenibacillus cookii	80.1142	823	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.09	99.09	0.93	0.93	2	-
GCF_002741055.1	s__Paenibacillus ihbetae	77.7923	286	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.87	98.87	0.95	0.95	2	-
GCF_900454495.1	s__Paenibacillus_A macerans	77.7278	207	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.51	99.09	0.97	0.93	8	-
GCF_001373415.1	s__Paenibacillus dakarensis	77.549	199	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011090185.1	s__Saccharibacillus alkalitolerans	76.774	105	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:45,087] [INFO] GTDB search result was written to GCF_004916975.1_ASM491697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:45,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:45,092] [INFO] DFAST_QC result json was written to GCF_004916975.1_ASM491697v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:45,092] [INFO] DFAST_QC completed!
[2024-01-24 12:16:45,092] [INFO] Total running time: 0h1m56s