[2024-01-24 14:15:32,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:32,318] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:32,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg97374f27-1ae8-45fb-a653-a2f031d601c5/dqc_reference
[2024-01-24 14:15:33,607] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:33,609] [INFO] Task started: Prodigal
[2024-01-24 14:15:33,611] [INFO] Running command: gunzip -c /var/lib/cwl/stg03c5b3db-4cb1-4773-8f5a-33b49dcb76c5/GCF_024722015.1_ASM2472201v1_genomic.fna.gz | prodigal -d GCF_024722015.1_ASM2472201v1_genomic.fna/cds.fna -a GCF_024722015.1_ASM2472201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:56,615] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:56,616] [INFO] Task started: HMMsearch
[2024-01-24 14:15:56,616] [INFO] Running command: hmmsearch --tblout GCF_024722015.1_ASM2472201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97374f27-1ae8-45fb-a653-a2f031d601c5/dqc_reference/reference_markers.hmm GCF_024722015.1_ASM2472201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:57,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:57,143] [INFO] Found 6/6 markers.
[2024-01-24 14:15:57,454] [INFO] Query marker FASTA was written to GCF_024722015.1_ASM2472201v1_genomic.fna/markers.fasta
[2024-01-24 14:15:57,454] [INFO] Task started: Blastn
[2024-01-24 14:15:57,454] [INFO] Running command: blastn -query GCF_024722015.1_ASM2472201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97374f27-1ae8-45fb-a653-a2f031d601c5/dqc_reference/reference_markers.fasta -out GCF_024722015.1_ASM2472201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:58,060] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:58,064] [INFO] Selected 25 target genomes.
[2024-01-24 14:15:58,064] [INFO] Target genome list was writen to GCF_024722015.1_ASM2472201v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:58,074] [INFO] Task started: fastANI
[2024-01-24 14:15:58,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg03c5b3db-4cb1-4773-8f5a-33b49dcb76c5/GCF_024722015.1_ASM2472201v1_genomic.fna.gz --refList GCF_024722015.1_ASM2472201v1_genomic.fna/target_genomes.txt --output GCF_024722015.1_ASM2472201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:29,700] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:29,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97374f27-1ae8-45fb-a653-a2f031d601c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:29,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97374f27-1ae8-45fb-a653-a2f031d601c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:29,717] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:16:29,717] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:16:29,717] [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 foliorum	strain=LMG 31456	GCA_013141765.1	2654974	2654974	type	True	86.158	1961	2896	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	78.9617	485	2896	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	78.869	201	2896	95	below_threshold
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	78.8116	770	2896	95	below_threshold
Paenibacillus rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	78.3398	396	2896	95	below_threshold
Paenibacillus xerothermodurans	strain=ATCC 27380	GCA_002220865.2	1977292	1977292	type	True	77.8879	229	2896	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.6836	380	2896	95	below_threshold
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	77.4412	177	2896	95	below_threshold
Paenibacillus eucommiae	strain=DSM 26048	GCA_017874215.1	1355755	1355755	type	True	77.3871	173	2896	95	below_threshold
Paenibacillus nasutitermitis	strain=CGMCC 1.15178	GCA_014641075.1	1652958	1652958	type	True	77.1677	115	2896	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	77.0778	150	2896	95	below_threshold
Paenibacillus guangzhouensis	strain=KCTC 33171	GCA_009363075.1	1473112	1473112	type	True	76.925	94	2896	95	below_threshold
Paenibacillus naphthalenovorans	strain=PR-N1	GCA_900099895.1	162209	162209	type	True	76.8379	162	2896	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	76.743	115	2896	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	76.741	71	2896	95	below_threshold
Paenibacillus crassostreae	strain=LPB0068	GCA_001857945.1	1763538	1763538	type	True	76.7332	60	2896	95	below_threshold
Paenibacillus algorifonticola	strain=XJ259	GCA_000971975.1	684063	684063	type	True	76.6892	112	2896	95	below_threshold
Paenibacillus crassostreae	strain=LPB0068	GCA_001637335.1	1763538	1763538	type	True	76.6842	57	2896	95	below_threshold
Paenibacillus roseus	strain=MAHUQ-46	GCA_016424485.1	2798579	2798579	type	True	76.4053	59	2896	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	75.9675	84	2896	95	below_threshold
Paenibacillus turpanensis	strain=YIM B00363	GCA_011421635.1	2689078	2689078	type	True	75.6921	59	2896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:29,719] [INFO] DFAST Taxonomy check result was written to GCF_024722015.1_ASM2472201v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:29,719] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:29,719] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:29,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97374f27-1ae8-45fb-a653-a2f031d601c5/dqc_reference/checkm_data
[2024-01-24 14:16:29,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:29,800] [INFO] Task started: CheckM
[2024-01-24 14:16:29,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024722015.1_ASM2472201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024722015.1_ASM2472201v1_genomic.fna/checkm_input GCF_024722015.1_ASM2472201v1_genomic.fna/checkm_result
[2024-01-24 14:17:36,115] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:36,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:36,143] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:36,144] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:36,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024722015.1_ASM2472201v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:36,145] [INFO] Task started: Blastn
[2024-01-24 14:17:36,145] [INFO] Running command: blastn -query GCF_024722015.1_ASM2472201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97374f27-1ae8-45fb-a653-a2f031d601c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_024722015.1_ASM2472201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:36,950] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:36,955] [INFO] Selected 27 target genomes.
[2024-01-24 14:17:36,955] [INFO] Target genome list was writen to GCF_024722015.1_ASM2472201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:37,011] [INFO] Task started: fastANI
[2024-01-24 14:17:37,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg03c5b3db-4cb1-4773-8f5a-33b49dcb76c5/GCF_024722015.1_ASM2472201v1_genomic.fna.gz --refList GCF_024722015.1_ASM2472201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024722015.1_ASM2472201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:18:13,822] [INFO] Task succeeded: fastANI
[2024-01-24 14:18:13,842] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:18:13,842] [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_013141765.1	s__Paenibacillus_S foliorum	86.1701	1959	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114475.1	s__Paenibacillus_S sp900114475	79.1207	475	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956045.1	s__Paenibacillus_S sp001956045	78.8753	527	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004354045.1	s__Paenibacillus_S piri	78.8009	767	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234615.1	s__Paenibacillus_S rigui	78.3362	395	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686845.1	s__Paenibacillus_S sp000686845	78.2538	419	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011440305.1	s__Paenibacillus_S sp011440305	78.2015	398	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002220865.2	s__Paenibacillus_S xerothermodurans	77.8838	230	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002042965.1	s__Paenibacillus_S sp002042965	77.8528	374	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	97.63	97.63	0.93	0.93	2	-
GCF_000722545.1	s__Paenibacillus_G tyrfis	77.3287	186	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.07	98.07	0.93	0.93	2	-
GCF_014641075.1	s__Paenibacillus_Z nasutitermitis	77.1058	114	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000985.1	s__Paenibacillus_G validus	77.0778	150	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.29	99.15	0.90	0.89	6	-
GCF_017874275.1	s__Paenibacillus_Z sepulcri	77.0372	135	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956095.1	s__Paenibacillus_C sp001956095	77.0334	97	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101595.1	s__Paenibacillus_G sp900101595	76.9935	143	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018998565.1	s__Paenibacillus_G sp018998565	76.9377	200	2896	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_009363075.1	s__Paenibacillus_K guangzhouensis	76.929	91	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099895.1	s__Paenibacillus_G naphthalenovorans	76.8782	162	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.27	98.99	0.91	0.86	5	-
GCF_900110075.1	s__Paenibacillus_Z sp900110075	76.7239	88	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001857945.1	s__Paenibacillus crassostreae	76.7097	59	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000971975.1	s__Paenibacillus_C algorifonticola	76.7006	113	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000380965.1	s__Paenibacillus_M ginsengihumi	76.1063	100	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705615.1	s__Paenibacillus_AB sp014705615	75.9719	82	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583765.1	s__Paenibacillus_C nanensis	75.8173	67	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011421635.1	s__Paenibacillus_AK turpanensis	75.6921	59	2896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AK	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:18:13,847] [INFO] GTDB search result was written to GCF_024722015.1_ASM2472201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:18:13,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:18:13,855] [INFO] DFAST_QC result json was written to GCF_024722015.1_ASM2472201v1_genomic.fna/dqc_result.json
[2024-01-24 14:18:13,856] [INFO] DFAST_QC completed!
[2024-01-24 14:18:13,856] [INFO] Total running time: 0h2m42s