[2024-01-24 14:55:07,950] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:07,952] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:07,952] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1991f63-b9f1-42e1-8b1e-2eafcfe05095/dqc_reference
[2024-01-24 14:55:09,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,614] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,615] [INFO] Running command: gunzip -c /var/lib/cwl/stgd46f5d98-3eaa-441d-86c8-a2abf5102357/GCF_001310895.1_ASM131089v1_genomic.fna.gz | prodigal -d GCF_001310895.1_ASM131089v1_genomic.fna/cds.fna -a GCF_001310895.1_ASM131089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:18,232] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:18,233] [INFO] Task started: HMMsearch
[2024-01-24 14:55:18,233] [INFO] Running command: hmmsearch --tblout GCF_001310895.1_ASM131089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1991f63-b9f1-42e1-8b1e-2eafcfe05095/dqc_reference/reference_markers.hmm GCF_001310895.1_ASM131089v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:18,544] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:18,545] [INFO] Found 6/6 markers.
[2024-01-24 14:55:18,579] [INFO] Query marker FASTA was written to GCF_001310895.1_ASM131089v1_genomic.fna/markers.fasta
[2024-01-24 14:55:18,579] [INFO] Task started: Blastn
[2024-01-24 14:55:18,579] [INFO] Running command: blastn -query GCF_001310895.1_ASM131089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1991f63-b9f1-42e1-8b1e-2eafcfe05095/dqc_reference/reference_markers.fasta -out GCF_001310895.1_ASM131089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:19,219] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:19,223] [INFO] Selected 23 target genomes.
[2024-01-24 14:55:19,224] [INFO] Target genome list was writen to GCF_001310895.1_ASM131089v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:19,238] [INFO] Task started: fastANI
[2024-01-24 14:55:19,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgd46f5d98-3eaa-441d-86c8-a2abf5102357/GCF_001310895.1_ASM131089v1_genomic.fna.gz --refList GCF_001310895.1_ASM131089v1_genomic.fna/target_genomes.txt --output GCF_001310895.1_ASM131089v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:34,911] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:34,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1991f63-b9f1-42e1-8b1e-2eafcfe05095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:34,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1991f63-b9f1-42e1-8b1e-2eafcfe05095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:34,927] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:34,927] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:34,928] [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 halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	100.0	1257	1260	95	conclusive
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	78.4783	137	1260	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.907	185	1260	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.5829	165	1260	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.5219	218	1260	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	77.4927	121	1260	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	77.4636	132	1260	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	77.4399	175	1260	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_014905475.1	1462526	1462526	suspected-type	True	77.4153	174	1260	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.3739	146	1260	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	77.1678	111	1260	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	77.1056	120	1260	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	77.0571	153	1260	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.033	135	1260	95	below_threshold
Thalassobacillus cyri	strain=CCM7597	GCA_900107755.1	571932	571932	type	True	77.0263	54	1260	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.9706	77	1260	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.945	148	1260	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	76.8691	59	1260	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.0543	50	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:35,059] [INFO] DFAST Taxonomy check result was written to GCF_001310895.1_ASM131089v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:35,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:35,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:35,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1991f63-b9f1-42e1-8b1e-2eafcfe05095/dqc_reference/checkm_data
[2024-01-24 14:55:35,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:35,101] [INFO] Task started: CheckM
[2024-01-24 14:55:35,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001310895.1_ASM131089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001310895.1_ASM131089v1_genomic.fna/checkm_input GCF_001310895.1_ASM131089v1_genomic.fna/checkm_result
[2024-01-24 14:56:04,805] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:04,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:04,828] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:04,829] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:04,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001310895.1_ASM131089v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:04,830] [INFO] Task started: Blastn
[2024-01-24 14:56:04,830] [INFO] Running command: blastn -query GCF_001310895.1_ASM131089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1991f63-b9f1-42e1-8b1e-2eafcfe05095/dqc_reference/reference_markers_gtdb.fasta -out GCF_001310895.1_ASM131089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:05,700] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:05,705] [INFO] Selected 23 target genomes.
[2024-01-24 14:56:05,705] [INFO] Target genome list was writen to GCF_001310895.1_ASM131089v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:05,722] [INFO] Task started: fastANI
[2024-01-24 14:56:05,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgd46f5d98-3eaa-441d-86c8-a2abf5102357/GCF_001310895.1_ASM131089v1_genomic.fna.gz --refList GCF_001310895.1_ASM131089v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001310895.1_ASM131089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:21,547] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:21,569] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:21,570] [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_001310895.1	s__Virgibacillus halodenitrificans	100.0	1257	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	98.29	98.21	0.89	0.88	7	conclusive
GCF_000725285.1	s__Virgibacillus sp000725285	91.01	1044	1260	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_001659985.1	s__Oceanobacillus sp001659985	78.7639	132	1260	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_003628445.1	s__Oceanobacillus bengalensis	78.4668	138	1260	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_016908155.1	s__Oceanobacillus caeni	78.1329	106	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_000612865.1	s__Virgibacillus picturae	77.816	173	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	97.99	95.34	0.93	0.90	5	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.7538	151	1260	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_016919725.1	s__Virgibacillus sp016919725	77.5592	178	1260	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_002287375.1	s__Virgibacillus_G profundi	77.5219	218	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002153375.1	s__Oceanobacillus rekensis	77.4825	133	1260	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_014905415.1	s__Virgibacillus salexigens	77.4107	178	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.53	99.42	0.93	0.91	9	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	77.3327	155	1260	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	-
GCA_004145795.1	s__Lentibacillus lipolyticus	77.3212	81	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369575.1	s__Oceanobacillus arenosus	77.1654	112	1260	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_003352005.1	s__Oceanobacillus zhaokaii	77.093	119	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	-
GCF_017873675.1	s__Lentibacillus litoralis	77.0757	150	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333215.1	s__Oceanobacillus sp018333215	77.0368	93	1260	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_009733865.1	s__Oceanobacillus salinisoli	76.9908	135	1260	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_900110695.1	s__Lentibacillus subterraneus	76.9707	148	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:21,571] [INFO] GTDB search result was written to GCF_001310895.1_ASM131089v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:21,572] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:21,577] [INFO] DFAST_QC result json was written to GCF_001310895.1_ASM131089v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:21,577] [INFO] DFAST_QC completed!
[2024-01-24 14:56:21,577] [INFO] Total running time: 0h1m14s