[2024-01-24 12:44:53,925] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:53,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:53,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg560d3f7a-ec65-4256-b009-700311800467/dqc_reference
[2024-01-24 12:44:55,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:55,274] [INFO] Task started: Prodigal
[2024-01-24 12:44:55,274] [INFO] Running command: gunzip -c /var/lib/cwl/stg23f9d0a4-44db-47a6-b3f4-c997f3917ead/GCF_001403875.1_Paenibacillus_ihumii_genomic.fna.gz | prodigal -d GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/cds.fna -a GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:12,664] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:12,665] [INFO] Task started: HMMsearch
[2024-01-24 12:45:12,665] [INFO] Running command: hmmsearch --tblout GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg560d3f7a-ec65-4256-b009-700311800467/dqc_reference/reference_markers.hmm GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:12,995] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:12,996] [INFO] Found 6/6 markers.
[2024-01-24 12:45:13,049] [INFO] Query marker FASTA was written to GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/markers.fasta
[2024-01-24 12:45:13,050] [INFO] Task started: Blastn
[2024-01-24 12:45:13,050] [INFO] Running command: blastn -query GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/markers.fasta -db /var/lib/cwl/stg560d3f7a-ec65-4256-b009-700311800467/dqc_reference/reference_markers.fasta -out GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:13,652] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:13,656] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:13,657] [INFO] Target genome list was writen to GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/target_genomes.txt
[2024-01-24 12:45:13,665] [INFO] Task started: fastANI
[2024-01-24 12:45:13,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg23f9d0a4-44db-47a6-b3f4-c997f3917ead/GCF_001403875.1_Paenibacillus_ihumii_genomic.fna.gz --refList GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/target_genomes.txt --output GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:29,926] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:29,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg560d3f7a-ec65-4256-b009-700311800467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:29,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg560d3f7a-ec65-4256-b009-700311800467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:29,951] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:29,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:29,952] [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 ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	100.0	1967	1968	95	conclusive
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	83.3166	1228	1968	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	82.2441	1067	1968	95	below_threshold
Paenibacillus lentus	strain=DSM 25539	GCA_003931855.1	1338368	1338368	type	True	82.0614	1060	1968	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	78.6799	433	1968	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	78.2948	428	1968	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	78.2049	360	1968	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	78.0528	372	1968	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	77.9576	123	1968	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.8029	298	1968	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.7239	262	1968	95	below_threshold
Paenibacillus tuaregi	strain=Marseille-P2472	GCA_900086655.1	1816681	1816681	type	True	77.719	236	1968	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	76.866	119	1968	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.6697	175	1968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:29,954] [INFO] DFAST Taxonomy check result was written to GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/tc_result.tsv
[2024-01-24 12:45:29,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:29,955] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:29,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg560d3f7a-ec65-4256-b009-700311800467/dqc_reference/checkm_data
[2024-01-24 12:45:29,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:30,015] [INFO] Task started: CheckM
[2024-01-24 12:45:30,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/checkm_input GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/checkm_result
[2024-01-24 12:46:22,564] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:22,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:22,589] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:22,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:22,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/markers.fasta)
[2024-01-24 12:46:22,590] [INFO] Task started: Blastn
[2024-01-24 12:46:22,590] [INFO] Running command: blastn -query GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/markers.fasta -db /var/lib/cwl/stg560d3f7a-ec65-4256-b009-700311800467/dqc_reference/reference_markers_gtdb.fasta -out GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:23,389] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:23,394] [INFO] Selected 8 target genomes.
[2024-01-24 12:46:23,394] [INFO] Target genome list was writen to GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:23,402] [INFO] Task started: fastANI
[2024-01-24 12:46:23,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg23f9d0a4-44db-47a6-b3f4-c997f3917ead/GCF_001403875.1_Paenibacillus_ihumii_genomic.fna.gz --refList GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/target_genomes_gtdb.txt --output GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:33,994] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:34,004] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:34,004] [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_001403875.1	s__Paenibacillus_A ihumii	100.0	1967	1968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009725165.1	s__Paenibacillus_A woosongensis	85.5031	1373	1968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	95.99	95.99	0.91	0.91	2	-
GCF_900155685.1	s__Paenibacillus_A bouchesdurhonensis	83.3407	1226	1968	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_000381905.1	s__Paenibacillus_A fonticola	82.242	1067	1968	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_003931855.1	s__Paenibacillus_A lentus	82.0672	1063	1968	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_003863965.1	s__Paenibacillus_A oralis	78.3296	429	1968	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_008084145.1	s__Paenibacillus_A faecis	78.226	423	1968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.85	97.85	0.92	0.92	2	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	78.0501	373	1968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:34,007] [INFO] GTDB search result was written to GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:34,008] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:34,013] [INFO] DFAST_QC result json was written to GCF_001403875.1_Paenibacillus_ihumii_genomic.fna/dqc_result.json
[2024-01-24 12:46:34,013] [INFO] DFAST_QC completed!
[2024-01-24 12:46:34,013] [INFO] Total running time: 0h1m40s