[2024-01-24 12:22:34,101] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg67063220-e916-40ca-9149-d32e1274c8d7/dqc_reference
[2024-01-24 12:22:35,385] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,386] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,386] [INFO] Running command: gunzip -c /var/lib/cwl/stgb13ee0e1-22cc-41b7-b63d-39ac78f74605/GCF_014644435.1_ASM1464443v1_genomic.fna.gz | prodigal -d GCF_014644435.1_ASM1464443v1_genomic.fna/cds.fna -a GCF_014644435.1_ASM1464443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:57,054] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:57,054] [INFO] Task started: HMMsearch
[2024-01-24 12:22:57,054] [INFO] Running command: hmmsearch --tblout GCF_014644435.1_ASM1464443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67063220-e916-40ca-9149-d32e1274c8d7/dqc_reference/reference_markers.hmm GCF_014644435.1_ASM1464443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:57,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:57,422] [INFO] Found 6/6 markers.
[2024-01-24 12:22:57,492] [INFO] Query marker FASTA was written to GCF_014644435.1_ASM1464443v1_genomic.fna/markers.fasta
[2024-01-24 12:22:57,493] [INFO] Task started: Blastn
[2024-01-24 12:22:57,493] [INFO] Running command: blastn -query GCF_014644435.1_ASM1464443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67063220-e916-40ca-9149-d32e1274c8d7/dqc_reference/reference_markers.fasta -out GCF_014644435.1_ASM1464443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:58,176] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:58,182] [INFO] Selected 25 target genomes.
[2024-01-24 12:22:58,183] [INFO] Target genome list was writen to GCF_014644435.1_ASM1464443v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:58,193] [INFO] Task started: fastANI
[2024-01-24 12:22:58,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgb13ee0e1-22cc-41b7-b63d-39ac78f74605/GCF_014644435.1_ASM1464443v1_genomic.fna.gz --refList GCF_014644435.1_ASM1464443v1_genomic.fna/target_genomes.txt --output GCF_014644435.1_ASM1464443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:29,663] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:29,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67063220-e916-40ca-9149-d32e1274c8d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:29,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67063220-e916-40ca-9149-d32e1274c8d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:29,688] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:29,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:29,688] [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 albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	100.0	2489	2497	95	conclusive
Paenibacillus sonchi	strain=X19-5	GCA_000316285.1	373687	373687	type	True	80.6998	795	2497	95	below_threshold
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	80.6576	830	2497	95	below_threshold
Paenibacillus graminis	strain=DSM 15220	GCA_000758705.1	189425	189425	type	True	80.562	965	2497	95	below_threshold
Paenibacillus riograndensis		GCA_000981585.1	483937	483937	type	True	80.5419	979	2497	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	80.5357	973	2497	95	below_threshold
Paenibacillus riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	80.5064	703	2497	95	below_threshold
Paenibacillus azotifigens	strain=LMG 29963	GCA_008635805.1	2047734	2047734	type	True	80.4189	934	2497	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	79.9852	886	2497	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	79.846	772	2497	95	below_threshold
Paenibacillus ihuae	strain=GD6	GCA_001368795.1	1232431	1232431	type	True	79.792	804	2497	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	79.6792	890	2497	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	79.6049	859	2497	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.5509	693	2497	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	79.3835	818	2497	95	below_threshold
Paenibacillus wynnii	strain=DSM 18334	GCA_000757885.1	268407	268407	type	True	79.323	589	2497	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	79.0505	767	2497	95	below_threshold
Paenibacillus tengchongensis	strain=SYSU G01003	GCA_008973665.1	2608684	2608684	type	True	78.836	645	2497	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.301	470	2497	95	below_threshold
Paenibacillus lemnae	strain=L7-75	GCA_012933385.1	1330551	1330551	type	True	77.1842	164	2497	95	below_threshold
Paenibacillus yonginensis	strain=DCY84	GCA_001685395.1	1462996	1462996	type	True	77.1592	166	2497	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.5951	162	2497	95	below_threshold
Gorillibacterium timonense	strain=SN4	GCA_001457415.1	1689269	1689269	type	True	76.1139	79	2497	95	below_threshold
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	75.7159	72	2497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,690] [INFO] DFAST Taxonomy check result was written to GCF_014644435.1_ASM1464443v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:29,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:29,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:29,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67063220-e916-40ca-9149-d32e1274c8d7/dqc_reference/checkm_data
[2024-01-24 12:23:29,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:29,768] [INFO] Task started: CheckM
[2024-01-24 12:23:29,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644435.1_ASM1464443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644435.1_ASM1464443v1_genomic.fna/checkm_input GCF_014644435.1_ASM1464443v1_genomic.fna/checkm_result
[2024-01-24 12:24:29,081] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:29,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:29,111] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:29,111] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:29,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644435.1_ASM1464443v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:29,112] [INFO] Task started: Blastn
[2024-01-24 12:24:29,112] [INFO] Running command: blastn -query GCF_014644435.1_ASM1464443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67063220-e916-40ca-9149-d32e1274c8d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644435.1_ASM1464443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:29,932] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:29,936] [INFO] Selected 23 target genomes.
[2024-01-24 12:24:29,936] [INFO] Target genome list was writen to GCF_014644435.1_ASM1464443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:29,948] [INFO] Task started: fastANI
[2024-01-24 12:24:29,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgb13ee0e1-22cc-41b7-b63d-39ac78f74605/GCF_014644435.1_ASM1464443v1_genomic.fna.gz --refList GCF_014644435.1_ASM1464443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644435.1_ASM1464443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:04,529] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:04,550] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:04,550] [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_014644435.1	s__Paenibacillus albidus	100.0	2489	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.34	96.34	0.80	0.80	2	conclusive
GCF_900102965.1	s__Paenibacillus jilunlii	80.6962	955	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.98	99.98	1.00	0.99	3	-
GCF_000758525.1	s__Paenibacillus sp000758525	80.5773	1003	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.46	97.46	0.89	0.89	2	-
GCF_000758705.1	s__Paenibacillus graminis	80.5751	962	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000981585.1	s__Paenibacillus riograndensis	80.5611	975	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	97.36	97.36	0.91	0.91	2	-
GCF_016772475.1	s__Paenibacillus sonchi	80.536	973	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	99.97	99.97	1.00	1.00	2	-
GCF_001909055.1	s__Paenibacillus helianthi	80.0455	875	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.61	95.31	0.90	0.83	4	-
GCF_013141775.1	s__Paenibacillus phytohabitans	79.9913	886	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.61	96.02	0.84	0.83	4	-
GCF_000758605.1	s__Paenibacillus sp000758605	79.8673	862	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086365.1	s__Paenibacillus sp017086365	79.8257	776	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001368795.1	s__Paenibacillus ihuae	79.7921	804	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000758665.1	s__Paenibacillus borealis	79.6717	894	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204885.1	s__Paenibacillus tritici	79.6254	855	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.22	98.22	0.93	0.93	2	-
GCF_000374185.1	s__Paenibacillus sp000374185	79.5935	854	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874765.1	s__Paenibacillus rhizoplanae	79.533	853	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723885.1	s__Paenibacillus camerounensis	79.3806	748	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.67	95.67	0.88	0.88	2	-
GCF_017874735.1	s__Paenibacillus silagei	79.3747	819	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
GCF_000757885.1	s__Paenibacillus wynnii	79.3175	588	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001955925.1	s__Paenibacillus sp001955925	79.1827	804	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.91	98.91	0.92	0.92	2	-
GCF_008973665.1	s__Paenibacillus tengchongensis	78.842	646	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060825.1	s__Paenibacillus_A sp003060825	77.6468	157	2497	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_018333315.1	s__Paenibacillus azoreducens	77.4062	218	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.74	97.74	0.88	0.88	2	-
GCF_001685395.1	s__Paenibacillus_A yonginensis	77.1592	166	2497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:04,552] [INFO] GTDB search result was written to GCF_014644435.1_ASM1464443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:04,552] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:04,557] [INFO] DFAST_QC result json was written to GCF_014644435.1_ASM1464443v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:04,557] [INFO] DFAST_QC completed!
[2024-01-24 12:25:04,558] [INFO] Total running time: 0h2m30s