[2024-01-24 10:47:24,176] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,179] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,179] [INFO] DQC Reference Directory: /var/lib/cwl/stga796b0ff-37e8-4671-808c-4589c3ee33fb/dqc_reference
[2024-01-24 10:47:26,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,384] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg62d8fdf6-c932-44b0-93e2-4a07e78d8f8b/GCF_002192415.1_ASM219241v1_genomic.fna.gz | prodigal -d GCF_002192415.1_ASM219241v1_genomic.fna/cds.fna -a GCF_002192415.1_ASM219241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:49,697] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:49,697] [INFO] Task started: HMMsearch
[2024-01-24 10:47:49,697] [INFO] Running command: hmmsearch --tblout GCF_002192415.1_ASM219241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga796b0ff-37e8-4671-808c-4589c3ee33fb/dqc_reference/reference_markers.hmm GCF_002192415.1_ASM219241v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:50,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:50,076] [INFO] Found 6/6 markers.
[2024-01-24 10:47:50,138] [INFO] Query marker FASTA was written to GCF_002192415.1_ASM219241v1_genomic.fna/markers.fasta
[2024-01-24 10:47:50,139] [INFO] Task started: Blastn
[2024-01-24 10:47:50,139] [INFO] Running command: blastn -query GCF_002192415.1_ASM219241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga796b0ff-37e8-4671-808c-4589c3ee33fb/dqc_reference/reference_markers.fasta -out GCF_002192415.1_ASM219241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:50,777] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:50,780] [INFO] Selected 26 target genomes.
[2024-01-24 10:47:50,781] [INFO] Target genome list was writen to GCF_002192415.1_ASM219241v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:50,815] [INFO] Task started: fastANI
[2024-01-24 10:47:50,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg62d8fdf6-c932-44b0-93e2-4a07e78d8f8b/GCF_002192415.1_ASM219241v1_genomic.fna.gz --refList GCF_002192415.1_ASM219241v1_genomic.fna/target_genomes.txt --output GCF_002192415.1_ASM219241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:28,773] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:28,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga796b0ff-37e8-4671-808c-4589c3ee33fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:28,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga796b0ff-37e8-4671-808c-4589c3ee33fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:28,798] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:28,799] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:28,799] [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 donghaensis	strain=KCTC 13049	GCA_002192415.1	414771	414771	type	True	100.0	2846	2847	95	conclusive
Paenibacillus albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	80.573	1015	2847	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	80.3816	966	2847	95	below_threshold
Paenibacillus graminis	strain=DSM 15220	GCA_000758705.1	189425	189425	type	True	80.1568	961	2847	95	below_threshold
Paenibacillus sonchi	strain=X19-5	GCA_000316285.1	373687	373687	type	True	80.1469	752	2847	95	below_threshold
Paenibacillus jilunlii	strain=CGMCC 1.10239	GCA_900102965.1	682956	682956	type	True	80.0838	923	2847	95	below_threshold
Paenibacillus jilunlii	strain=DSM 23019	GCA_001546055.1	682956	682956	type	True	80.0562	914	2847	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	80.0461	985	2847	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	79.9817	989	2847	95	below_threshold
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	79.9124	810	2847	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	79.8878	800	2847	95	below_threshold
Paenibacillus azotifigens	strain=LMG 29963	GCA_008635805.1	2047734	2047734	type	True	79.8393	924	2847	95	below_threshold
Paenibacillus ihuae	strain=GD6	GCA_001368795.1	1232431	1232431	type	True	79.7215	857	2847	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	79.4881	933	2847	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	79.3696	910	2847	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.2809	621	2847	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	79.2389	869	2847	95	below_threshold
Paenibacillus sophorae	strain=DSM 23020	GCA_018966525.1	1333845	1333845	type	True	78.5748	485	2847	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.326	455	2847	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	78.3224	179	2847	95	below_threshold
Paenibacillus algorifonticola	strain=XJ259	GCA_000971975.1	684063	684063	type	True	78.3057	180	2847	95	below_threshold
Paenibacillus sophorae	strain=CGMCC 1.10238	GCA_900110315.1	1333845	1333845	type	True	78.3037	469	2847	95	below_threshold
Paenibacillus stellifer	strain=DSM 14472	GCA_000758685.1	169760	169760	type	True	78.2633	487	2847	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	78.0154	458	2847	95	below_threshold
Paenibacillus zanthoxyli	strain=JH29	GCA_000520715.1	369399	369399	type	True	77.9129	397	2847	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	76.1823	103	2847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:28,800] [INFO] DFAST Taxonomy check result was written to GCF_002192415.1_ASM219241v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:28,801] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:28,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:28,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga796b0ff-37e8-4671-808c-4589c3ee33fb/dqc_reference/checkm_data
[2024-01-24 10:48:28,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:28,877] [INFO] Task started: CheckM
[2024-01-24 10:48:28,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002192415.1_ASM219241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002192415.1_ASM219241v1_genomic.fna/checkm_input GCF_002192415.1_ASM219241v1_genomic.fna/checkm_result
[2024-01-24 10:49:36,924] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:36,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:36,957] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:36,957] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:36,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002192415.1_ASM219241v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:36,958] [INFO] Task started: Blastn
[2024-01-24 10:49:36,958] [INFO] Running command: blastn -query GCF_002192415.1_ASM219241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga796b0ff-37e8-4671-808c-4589c3ee33fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002192415.1_ASM219241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:37,836] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:37,842] [INFO] Selected 22 target genomes.
[2024-01-24 10:49:37,843] [INFO] Target genome list was writen to GCF_002192415.1_ASM219241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:37,882] [INFO] Task started: fastANI
[2024-01-24 10:49:37,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg62d8fdf6-c932-44b0-93e2-4a07e78d8f8b/GCF_002192415.1_ASM219241v1_genomic.fna.gz --refList GCF_002192415.1_ASM219241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002192415.1_ASM219241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:13,029] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:13,048] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:13,049] [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_002192415.1	s__Paenibacillus donghaensis	100.0	2846	2847	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_000758525.1	s__Paenibacillus sp000758525	80.8665	1077	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.46	97.46	0.89	0.89	2	-
GCF_014644435.1	s__Paenibacillus albidus	80.5997	1013	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.34	96.34	0.80	0.80	2	-
GCF_000758705.1	s__Paenibacillus graminis	80.1705	959	2847	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	80.0735	987	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102965.1	s__Paenibacillus jilunlii	80.0698	925	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.98	99.98	1.00	0.99	3	-
GCF_000758605.1	s__Paenibacillus sp000758605	80.0545	969	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141775.1	s__Paenibacillus phytohabitans	79.962	994	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.61	96.02	0.84	0.83	4	-
GCF_017086365.1	s__Paenibacillus sp017086365	79.9183	805	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374185.1	s__Paenibacillus sp000374185	79.8139	896	2847	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	79.714	856	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017874765.1	s__Paenibacillus rhizoplanae	79.5041	914	2847	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	79.4852	933	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.22	98.22	0.93	0.93	2	-
GCF_017874735.1	s__Paenibacillus silagei	79.3756	908	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
GCF_001955925.1	s__Paenibacillus sp001955925	79.3257	883	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.91	98.91	0.92	0.92	2	-
GCF_000758625.1	s__Paenibacillus sp000758625	79.3027	880	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013359945.1	s__Paenibacillus sp013359945	79.2739	621	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756615.1	s__Paenibacillus durus	78.8006	459	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018966525.1	s__Paenibacillus sophorae	78.5748	485	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000520715.1	s__Paenibacillus zanthoxyli	77.921	396	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873605.1	s__Paenibacillus lactis	76.7977	212	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.99	97.11	0.89	0.86	16	-
GCF_002272015.1	s__Paenibacillus campinasensis	76.5426	199	2847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.23	99.19	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:13,051] [INFO] GTDB search result was written to GCF_002192415.1_ASM219241v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:13,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:13,058] [INFO] DFAST_QC result json was written to GCF_002192415.1_ASM219241v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:13,058] [INFO] DFAST_QC completed!
[2024-01-24 10:50:13,058] [INFO] Total running time: 0h2m49s