[2024-01-24 11:43:25,077] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,084] [INFO] DQC Reference Directory: /var/lib/cwl/stgaded1cef-9edb-4282-ab6c-d8deae852878/dqc_reference
[2024-01-24 11:43:30,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,060] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e7490f0-c96e-4e44-91ec-2044ed2a365a/GCF_014905475.1_ASM1490547v1_genomic.fna.gz | prodigal -d GCF_014905475.1_ASM1490547v1_genomic.fna/cds.fna -a GCF_014905475.1_ASM1490547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:39,134] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:39,134] [INFO] Task started: HMMsearch
[2024-01-24 11:43:39,134] [INFO] Running command: hmmsearch --tblout GCF_014905475.1_ASM1490547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaded1cef-9edb-4282-ab6c-d8deae852878/dqc_reference/reference_markers.hmm GCF_014905475.1_ASM1490547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:39,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:39,445] [INFO] Found 6/6 markers.
[2024-01-24 11:43:39,493] [INFO] Query marker FASTA was written to GCF_014905475.1_ASM1490547v1_genomic.fna/markers.fasta
[2024-01-24 11:43:39,493] [INFO] Task started: Blastn
[2024-01-24 11:43:39,494] [INFO] Running command: blastn -query GCF_014905475.1_ASM1490547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaded1cef-9edb-4282-ab6c-d8deae852878/dqc_reference/reference_markers.fasta -out GCF_014905475.1_ASM1490547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:40,083] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:40,087] [INFO] Selected 34 target genomes.
[2024-01-24 11:43:40,088] [INFO] Target genome list was writen to GCF_014905475.1_ASM1490547v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:40,099] [INFO] Task started: fastANI
[2024-01-24 11:43:40,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e7490f0-c96e-4e44-91ec-2044ed2a365a/GCF_014905475.1_ASM1490547v1_genomic.fna.gz --refList GCF_014905475.1_ASM1490547v1_genomic.fna/target_genomes.txt --output GCF_014905475.1_ASM1490547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:59,771] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:59,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaded1cef-9edb-4282-ab6c-d8deae852878/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:59,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaded1cef-9edb-4282-ab6c-d8deae852878/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:59,787] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:43:59,787] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:59,787] [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
Virgibacillus massiliensis	strain=Vm-5	GCA_014905475.1	1462526	1462526	suspected-type	True	100.0	1439	1440	95	conclusive
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	99.9881	1435	1440	95	conclusive
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	77.6779	242	1440	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	77.6709	240	1440	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_018075365.1	1473	1473	type	True	77.6014	246	1440	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.4242	180	1440	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.3457	180	1440	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.2416	151	1440	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.1028	130	1440	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	77.0649	153	1440	95	below_threshold
Oceanobacillus sojae	strain=NBRC 105379	GCA_007991515.1	582851	582851	type	True	76.9991	91	1440	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	76.975	140	1440	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	76.9633	146	1440	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	76.9377	143	1440	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	76.82	82	1440	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.398	75	1440	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.0703	59	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:59,789] [INFO] DFAST Taxonomy check result was written to GCF_014905475.1_ASM1490547v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:59,789] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:59,789] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:59,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaded1cef-9edb-4282-ab6c-d8deae852878/dqc_reference/checkm_data
[2024-01-24 11:43:59,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:59,840] [INFO] Task started: CheckM
[2024-01-24 11:43:59,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014905475.1_ASM1490547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014905475.1_ASM1490547v1_genomic.fna/checkm_input GCF_014905475.1_ASM1490547v1_genomic.fna/checkm_result
[2024-01-24 11:44:33,084] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:33,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 15.34%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:33,107] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:33,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:33,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014905475.1_ASM1490547v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:33,108] [INFO] Task started: Blastn
[2024-01-24 11:44:33,108] [INFO] Running command: blastn -query GCF_014905475.1_ASM1490547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaded1cef-9edb-4282-ab6c-d8deae852878/dqc_reference/reference_markers_gtdb.fasta -out GCF_014905475.1_ASM1490547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:33,919] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:33,929] [INFO] Selected 33 target genomes.
[2024-01-24 11:44:33,929] [INFO] Target genome list was writen to GCF_014905475.1_ASM1490547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:33,957] [INFO] Task started: fastANI
[2024-01-24 11:44:33,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e7490f0-c96e-4e44-91ec-2044ed2a365a/GCF_014905475.1_ASM1490547v1_genomic.fna.gz --refList GCF_014905475.1_ASM1490547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014905475.1_ASM1490547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:54,089] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:54,106] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:54,106] [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_014905415.1	s__Virgibacillus salexigens	99.5405	1312	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.53	99.42	0.93	0.91	9	conclusive
GCF_016919725.1	s__Virgibacillus sp016919725	78.9916	514	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_900166595.1	s__Virgibacillus dokdonensis	77.8316	247	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.95	98.88	0.93	0.90	3	-
GCF_018916875.1	s__Virgibacillus proomii_B	77.7736	229	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612345.1	s__Virgibacillus sp003612345	77.6176	248	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	100.00	100.00	1.00	0.99	4	-
GCF_018075365.1	s__Virgibacillus pantothenticus	77.6014	246	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.44	97.53	0.92	0.86	18	-
GCF_900162615.1	s__Virgibacillus proomii_A	77.4928	282	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	77.4357	147	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129865.1	s__Virgibacillus chiguensis	77.4012	251	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.02	97.78	0.91	0.87	3	-
GCF_900111445.1	s__Ornithinibacillus limi	77.2528	137	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638995.1	s__Virgibacillus_E oceani	77.2416	151	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482485.1	s__Ornithinibacillus globulus	77.1449	127	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991515.1	s__Oceanobacillus sojae	77.0282	90	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.95	98.95	0.93	0.93	2	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.0218	178	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176885.1	s__Oceanobacillus senegalensis	76.975	140	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993955.1	s__YIM-98839 sp010993955	76.9377	143	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628505.1	s__Oceanobacillus halophilus	76.9341	146	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993965.1	s__Gracilibacillus sp010993965	76.5022	67	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650095.1	s__Gracilibacillus sp002797295	76.2465	83	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_003726095.1	s__Niallia circulans_A	76.1359	60	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.27	98.85	0.92	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:54,108] [INFO] GTDB search result was written to GCF_014905475.1_ASM1490547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:54,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:54,112] [INFO] DFAST_QC result json was written to GCF_014905475.1_ASM1490547v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:54,113] [INFO] DFAST_QC completed!
[2024-01-24 11:44:54,113] [INFO] Total running time: 0h1m29s