[2024-01-24 13:48:58,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:58,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:58,756] [INFO] DQC Reference Directory: /var/lib/cwl/stge6a3f2e5-6d6e-4e6f-8a7f-4dc93175c5c8/dqc_reference
[2024-01-24 13:49:00,116] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,118] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,118] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a2d9518-ed06-4a5c-8e45-8073b49bf1d5/GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna.gz | prodigal -d GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/cds.fna -a GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:18,104] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:18,104] [INFO] Task started: HMMsearch
[2024-01-24 13:49:18,104] [INFO] Running command: hmmsearch --tblout GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6a3f2e5-6d6e-4e6f-8a7f-4dc93175c5c8/dqc_reference/reference_markers.hmm GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:18,476] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:18,478] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2a2d9518-ed06-4a5c-8e45-8073b49bf1d5/GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna.gz]
[2024-01-24 13:49:18,536] [INFO] Query marker FASTA was written to GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/markers.fasta
[2024-01-24 13:49:18,536] [INFO] Task started: Blastn
[2024-01-24 13:49:18,537] [INFO] Running command: blastn -query GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stge6a3f2e5-6d6e-4e6f-8a7f-4dc93175c5c8/dqc_reference/reference_markers.fasta -out GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:19,190] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:19,193] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:19,194] [INFO] Target genome list was writen to GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/target_genomes.txt
[2024-01-24 13:49:19,199] [INFO] Task started: fastANI
[2024-01-24 13:49:19,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a2d9518-ed06-4a5c-8e45-8073b49bf1d5/GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna.gz --refList GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/target_genomes.txt --output GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:42,034] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:42,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6a3f2e5-6d6e-4e6f-8a7f-4dc93175c5c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:42,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6a3f2e5-6d6e-4e6f-8a7f-4dc93175c5c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:42,048] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:42,049] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:42,049] [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 ihuae	strain=GD6	GCA_001368795.1	1232431	1232431	type	True	99.9999	2227	2234	95	conclusive
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	94.0313	1724	2234	95	below_threshold
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	82.6746	1360	2234	95	below_threshold
Paenibacillus jilunlii	strain=CGMCC 1.10239	GCA_900102965.1	682956	682956	type	True	81.0236	1087	2234	95	below_threshold
Paenibacillus azotifigens	strain=LMG 29963	GCA_008635805.1	2047734	2047734	type	True	81.017	1052	2234	95	below_threshold
Paenibacillus jilunlii	strain=DSM 23019	GCA_001546055.1	682956	682956	type	True	81.0149	1068	2234	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	80.98	1155	2234	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	80.9658	1139	2234	95	below_threshold
Paenibacillus riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	80.876	822	2234	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	80.8507	1111	2234	95	below_threshold
Paenibacillus riograndensis		GCA_000981585.1	483937	483937	type	True	80.8096	1109	2234	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	80.3928	1047	2234	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	80.3248	1012	2234	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	79.9034	919	2234	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.433	599	2234	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.3402	467	2234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:42,090] [INFO] DFAST Taxonomy check result was written to GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/tc_result.tsv
[2024-01-24 13:49:42,091] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:42,091] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:42,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6a3f2e5-6d6e-4e6f-8a7f-4dc93175c5c8/dqc_reference/checkm_data
[2024-01-24 13:49:42,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:42,160] [INFO] Task started: CheckM
[2024-01-24 13:49:42,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/checkm_input GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/checkm_result
[2024-01-24 13:50:34,157] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:34,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:34,183] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:34,184] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:34,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/markers.fasta)
[2024-01-24 13:50:34,185] [INFO] Task started: Blastn
[2024-01-24 13:50:34,185] [INFO] Running command: blastn -query GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stge6a3f2e5-6d6e-4e6f-8a7f-4dc93175c5c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:34,985] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:34,989] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:34,989] [INFO] Target genome list was writen to GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:35,000] [INFO] Task started: fastANI
[2024-01-24 13:50:35,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a2d9518-ed06-4a5c-8e45-8073b49bf1d5/GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna.gz --refList GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/target_genomes_gtdb.txt --output GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:54,597] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:54,614] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:54,615] [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_001368795.1	s__Paenibacillus ihuae	99.9999	2227	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017086365.1	s__Paenibacillus sp017086365	94.0236	1725	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517085.1	s__Paenibacillus sp001517085	82.8331	1370	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099765.1	s__Paenibacillus typhae	82.6903	1359	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.38	98.38	0.94	0.94	2	-
GCF_000758625.1	s__Paenibacillus sp000758625	82.3824	1311	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000723885.1	s__Paenibacillus camerounensis	82.2952	1251	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.67	95.67	0.88	0.88	2	-
GCF_000758525.1	s__Paenibacillus sp000758525	81.8484	1236	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.46	97.46	0.89	0.89	2	-
GCF_000758605.1	s__Paenibacillus sp000758605	81.0505	1198	2234	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	81.0058	1088	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.98	99.98	1.00	0.99	3	-
GCF_013141775.1	s__Paenibacillus phytohabitans	80.9797	1136	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.61	96.02	0.84	0.83	4	-
GCF_000758665.1	s__Paenibacillus borealis	80.9677	1157	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874735.1	s__Paenibacillus silagei	80.2951	1015	2234	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:54,616] [INFO] GTDB search result was written to GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:54,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:54,624] [INFO] DFAST_QC result json was written to GCF_001368795.1_Paenibacillus_reamassiliensis_genomic.fna/dqc_result.json
[2024-01-24 13:50:54,624] [INFO] DFAST_QC completed!
[2024-01-24 13:50:54,625] [INFO] Total running time: 0h1m56s