[2024-01-24 13:58:10,896] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,899] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ee0cf4d-d406-4705-a3c1-a0ec6fcfe256/dqc_reference
[2024-01-24 13:58:12,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,099] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,100] [INFO] Running command: gunzip -c /var/lib/cwl/stgb647d2b3-01c2-4a09-a789-3c285f731015/GCF_005765165.1_ASM576516v1_genomic.fna.gz | prodigal -d GCF_005765165.1_ASM576516v1_genomic.fna/cds.fna -a GCF_005765165.1_ASM576516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:31,560] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:31,560] [INFO] Task started: HMMsearch
[2024-01-24 13:58:31,560] [INFO] Running command: hmmsearch --tblout GCF_005765165.1_ASM576516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ee0cf4d-d406-4705-a3c1-a0ec6fcfe256/dqc_reference/reference_markers.hmm GCF_005765165.1_ASM576516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:31,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:31,915] [INFO] Found 6/6 markers.
[2024-01-24 13:58:31,975] [INFO] Query marker FASTA was written to GCF_005765165.1_ASM576516v1_genomic.fna/markers.fasta
[2024-01-24 13:58:31,975] [INFO] Task started: Blastn
[2024-01-24 13:58:31,975] [INFO] Running command: blastn -query GCF_005765165.1_ASM576516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ee0cf4d-d406-4705-a3c1-a0ec6fcfe256/dqc_reference/reference_markers.fasta -out GCF_005765165.1_ASM576516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:32,681] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:32,685] [INFO] Selected 26 target genomes.
[2024-01-24 13:58:32,685] [INFO] Target genome list was writen to GCF_005765165.1_ASM576516v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:32,698] [INFO] Task started: fastANI
[2024-01-24 13:58:32,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgb647d2b3-01c2-4a09-a789-3c285f731015/GCF_005765165.1_ASM576516v1_genomic.fna.gz --refList GCF_005765165.1_ASM576516v1_genomic.fna/target_genomes.txt --output GCF_005765165.1_ASM576516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:01,363] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:01,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ee0cf4d-d406-4705-a3c1-a0ec6fcfe256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:01,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ee0cf4d-d406-4705-a3c1-a0ec6fcfe256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:01,383] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:01,384] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:01,384] [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 antri	strain=SYSU K30003	GCA_005765165.1	2582848	2582848	type	True	100.0	2356	2361	95	conclusive
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	77.4732	290	2361	95	below_threshold
Thermobacillus composti	strain=KWC4	GCA_000227705.3	377615	377615	type	True	77.3812	298	2361	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	77.3216	398	2361	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	77.2768	361	2361	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.2364	445	2361	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.2137	337	2361	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	77.2127	292	2361	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	77.1452	439	2361	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	77.0828	329	2361	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.0727	336	2361	95	below_threshold
Paenibacillus pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	77.0718	371	2361	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	77.06	378	2361	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.9128	162	2361	95	below_threshold
Paenibacillus thermoaerophilus	strain=DSM 26310	GCA_005938195.1	1215385	1215385	type	True	76.8151	199	2361	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	76.7796	292	2361	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	76.7695	346	2361	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.7129	155	2361	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.5551	101	2361	95	below_threshold
Paenibacillus contaminans	strain=CKOBP-6	GCA_003285015.1	450362	450362	type	True	76.512	209	2361	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	76.2824	185	2361	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.1205	151	2361	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:01,385] [INFO] DFAST Taxonomy check result was written to GCF_005765165.1_ASM576516v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:01,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:01,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:01,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ee0cf4d-d406-4705-a3c1-a0ec6fcfe256/dqc_reference/checkm_data
[2024-01-24 13:59:01,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:01,455] [INFO] Task started: CheckM
[2024-01-24 13:59:01,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005765165.1_ASM576516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005765165.1_ASM576516v1_genomic.fna/checkm_input GCF_005765165.1_ASM576516v1_genomic.fna/checkm_result
[2024-01-24 13:59:53,477] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:53,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:53,498] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:53,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:53,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005765165.1_ASM576516v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:53,499] [INFO] Task started: Blastn
[2024-01-24 13:59:53,499] [INFO] Running command: blastn -query GCF_005765165.1_ASM576516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ee0cf4d-d406-4705-a3c1-a0ec6fcfe256/dqc_reference/reference_markers_gtdb.fasta -out GCF_005765165.1_ASM576516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:54,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:54,457] [INFO] Selected 22 target genomes.
[2024-01-24 13:59:54,457] [INFO] Target genome list was writen to GCF_005765165.1_ASM576516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:54,476] [INFO] Task started: fastANI
[2024-01-24 13:59:54,476] [INFO] Running command: fastANI --query /var/lib/cwl/stgb647d2b3-01c2-4a09-a789-3c285f731015/GCF_005765165.1_ASM576516v1_genomic.fna.gz --refList GCF_005765165.1_ASM576516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005765165.1_ASM576516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:17,058] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:17,073] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:17,074] [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_005765165.1	s__Paenibacillus_AE antri	100.0	2356	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AE	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016482785.1	s__Paenibacillus_AE sp016482785	77.5234	322	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907165215.1	s__Thermobacillus xylanilyticus	77.4639	291	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	-
GCF_014705655.1	s__Paenibacillus_C sp014705655	77.435	393	2361	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_014212175.1	s__Cohnella xylanilytica	77.3217	398	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_014212125.1	s__Cohnella nanjingensis	77.2922	359	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829455.1	s__VKM-B-2647 sp000829455	77.2624	287	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__VKM-B-2647	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	77.1986	339	2361	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_003217775.1	s__Paenibacillus_AB flagellatus	77.1261	444	2361	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_004801405.1	s__Cohnella sp004801405	77.0911	328	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422485.1	s__Paenibacillus_O pasadenensis	77.0861	376	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.23	98.68	0.94	0.90	4	-
GCF_019091135.1	s__Cohnella sp019091135	76.8564	352	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938195.1	s__Paenibacillus_W thermoaerophilus	76.8137	199	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Reconcilibacillaceae;g__Paenibacillus_W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380965.1	s__Paenibacillus_M ginsengihumi	76.811	288	2361	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_014705605.1	s__Paenibacillus_D sp014705605	76.6172	249	2361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265175.1	s__Paenibacillus_AB hemerocallicola	76.5651	255	2361	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_018998565.1	s__Paenibacillus_G sp018998565	76.5299	199	2361	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_900100345.1	s__Paenibacillus_G tianmuensis	76.2833	185	2361	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:17,075] [INFO] GTDB search result was written to GCF_005765165.1_ASM576516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:17,076] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:17,080] [INFO] DFAST_QC result json was written to GCF_005765165.1_ASM576516v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:17,081] [INFO] DFAST_QC completed!
[2024-01-24 14:00:17,081] [INFO] Total running time: 0h2m6s