[2024-01-24 12:47:23,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:23,996] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:23,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg68aa7ae6-0786-442e-89f1-4518ada1cb54/dqc_reference
[2024-01-24 12:47:25,282] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:25,283] [INFO] Task started: Prodigal
[2024-01-24 12:47:25,283] [INFO] Running command: gunzip -c /var/lib/cwl/stgf646f687-6d6a-4b7e-a245-da8b45afab1e/GCF_009757775.1_ASM975777v1_genomic.fna.gz | prodigal -d GCF_009757775.1_ASM975777v1_genomic.fna/cds.fna -a GCF_009757775.1_ASM975777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:39,683] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:39,683] [INFO] Task started: HMMsearch
[2024-01-24 12:47:39,683] [INFO] Running command: hmmsearch --tblout GCF_009757775.1_ASM975777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68aa7ae6-0786-442e-89f1-4518ada1cb54/dqc_reference/reference_markers.hmm GCF_009757775.1_ASM975777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:40,033] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:40,035] [INFO] Found 6/6 markers.
[2024-01-24 12:47:40,104] [INFO] Query marker FASTA was written to GCF_009757775.1_ASM975777v1_genomic.fna/markers.fasta
[2024-01-24 12:47:40,105] [INFO] Task started: Blastn
[2024-01-24 12:47:40,105] [INFO] Running command: blastn -query GCF_009757775.1_ASM975777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68aa7ae6-0786-442e-89f1-4518ada1cb54/dqc_reference/reference_markers.fasta -out GCF_009757775.1_ASM975777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:40,731] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:40,736] [INFO] Selected 25 target genomes.
[2024-01-24 12:47:40,737] [INFO] Target genome list was writen to GCF_009757775.1_ASM975777v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:40,745] [INFO] Task started: fastANI
[2024-01-24 12:47:40,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgf646f687-6d6a-4b7e-a245-da8b45afab1e/GCF_009757775.1_ASM975777v1_genomic.fna.gz --refList GCF_009757775.1_ASM975777v1_genomic.fna/target_genomes.txt --output GCF_009757775.1_ASM975777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:07,749] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:07,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68aa7ae6-0786-442e-89f1-4518ada1cb54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:07,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68aa7ae6-0786-442e-89f1-4518ada1cb54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:07,775] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:07,775] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:07,775] [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 lutrae	strain=N10	GCA_009757775.1	2078573	2078573	type	True	100.0	1823	1824	95	conclusive
Paenibacillus chitinolyticus	strain=NBRC 15660	GCA_000739915.1	79263	79263	type	True	79.7669	644	1824	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_022811565.1	1406	1406	type	True	77.8026	60	1824	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	77.3372	84	1824	95	below_threshold
Paenibacillus ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	77.322	126	1824	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.2827	91	1824	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.2555	67	1824	95	below_threshold
Paenibacillus marchantiophytorum	strain=CGMCC 1.15043	GCA_014640555.1	1619310	1619310	type	True	77.2369	126	1824	95	below_threshold
Paenibacillus xerothermodurans	strain=ATCC 27380	GCA_002220865.2	1977292	1977292	type	True	76.9237	64	1824	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	76.8962	118	1824	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	76.8954	146	1824	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.8905	84	1824	95	below_threshold
Paenibacillus macerans	strain=NCTC6355	GCA_900454495.1	44252	44252	type	True	76.8897	85	1824	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	76.863	110	1824	95	below_threshold
Paenibacillus athensensis	strain=MEC069	GCA_004514475.2	1967502	1967502	type	True	76.849	119	1824	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.8122	66	1824	95	below_threshold
Paenibacillus tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	76.7861	72	1824	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	76.6756	99	1824	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	76.6204	70	1824	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	76.439	82	1824	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	76.4295	142	1824	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.2619	120	1824	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	76.1986	102	1824	95	below_threshold
Paenibacillus zanthoxyli	strain=JH29	GCA_000520715.1	369399	369399	type	True	76.0512	64	1824	95	below_threshold
Paenibacillus thermoaerophilus	strain=DSM 26310	GCA_005938195.1	1215385	1215385	type	True	75.6753	59	1824	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:07,777] [INFO] DFAST Taxonomy check result was written to GCF_009757775.1_ASM975777v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:07,778] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:07,779] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:07,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68aa7ae6-0786-442e-89f1-4518ada1cb54/dqc_reference/checkm_data
[2024-01-24 12:48:07,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:07,835] [INFO] Task started: CheckM
[2024-01-24 12:48:07,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009757775.1_ASM975777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009757775.1_ASM975777v1_genomic.fna/checkm_input GCF_009757775.1_ASM975777v1_genomic.fna/checkm_result
[2024-01-24 12:48:53,174] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:53,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:53,199] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:53,199] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:53,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009757775.1_ASM975777v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:53,200] [INFO] Task started: Blastn
[2024-01-24 12:48:53,201] [INFO] Running command: blastn -query GCF_009757775.1_ASM975777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68aa7ae6-0786-442e-89f1-4518ada1cb54/dqc_reference/reference_markers_gtdb.fasta -out GCF_009757775.1_ASM975777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:53,962] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:53,966] [INFO] Selected 11 target genomes.
[2024-01-24 12:48:53,967] [INFO] Target genome list was writen to GCF_009757775.1_ASM975777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:53,975] [INFO] Task started: fastANI
[2024-01-24 12:48:53,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgf646f687-6d6a-4b7e-a245-da8b45afab1e/GCF_009757775.1_ASM975777v1_genomic.fna.gz --refList GCF_009757775.1_ASM975777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009757775.1_ASM975777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:06,951] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:06,965] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:06,965] [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_009757775.1	s__Paenibacillus_F sp009757775	100.0	1823	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001541095.1	s__Paenibacillus_F sp001541095	93.6743	1638	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739915.1	s__Paenibacillus_F chitinolyticus	79.7749	643	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107975.1	s__Paenibacillus_F sp900107975	79.7135	630	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411255.1	s__Paenibacillus_F sp000411255	79.6466	633	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	99.59	98.79	0.98	0.94	4	-
GCF_003863965.1	s__Paenibacillus_A oralis	77.2906	83	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001399685.1	s__Paenibacillus_G sp001399685	77.2708	150	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104695.1	s__Paenibacillus_AI sp900104695	77.1474	95	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454495.1	s__Paenibacillus_A macerans	76.9254	86	1824	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_004000785.1	s__Paenibacillus_G ehimensis	76.4295	142	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
GCF_003955665.1	s__Paenibacillus_E whitsoniae	76.4061	111	1824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:06,967] [INFO] GTDB search result was written to GCF_009757775.1_ASM975777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:06,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:06,974] [INFO] DFAST_QC result json was written to GCF_009757775.1_ASM975777v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:06,974] [INFO] DFAST_QC completed!
[2024-01-24 12:49:06,974] [INFO] Total running time: 0h1m43s