[2024-01-24 13:57:16,574] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,576] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,576] [INFO] DQC Reference Directory: /var/lib/cwl/stgec894d93-04a3-482e-8cc3-44bb64a051d8/dqc_reference
[2024-01-24 13:57:17,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,943] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg87c2cb67-d740-485d-9ed0-7301256c09bd/GCF_022095695.1_ASM2209569v1_genomic.fna.gz | prodigal -d GCF_022095695.1_ASM2209569v1_genomic.fna/cds.fna -a GCF_022095695.1_ASM2209569v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:26,463] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:26,463] [INFO] Task started: HMMsearch
[2024-01-24 13:57:26,464] [INFO] Running command: hmmsearch --tblout GCF_022095695.1_ASM2209569v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec894d93-04a3-482e-8cc3-44bb64a051d8/dqc_reference/reference_markers.hmm GCF_022095695.1_ASM2209569v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:26,790] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:26,791] [INFO] Found 6/6 markers.
[2024-01-24 13:57:26,824] [INFO] Query marker FASTA was written to GCF_022095695.1_ASM2209569v1_genomic.fna/markers.fasta
[2024-01-24 13:57:26,825] [INFO] Task started: Blastn
[2024-01-24 13:57:26,825] [INFO] Running command: blastn -query GCF_022095695.1_ASM2209569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec894d93-04a3-482e-8cc3-44bb64a051d8/dqc_reference/reference_markers.fasta -out GCF_022095695.1_ASM2209569v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:27,421] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:27,428] [INFO] Selected 20 target genomes.
[2024-01-24 13:57:27,428] [INFO] Target genome list was writen to GCF_022095695.1_ASM2209569v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:27,435] [INFO] Task started: fastANI
[2024-01-24 13:57:27,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg87c2cb67-d740-485d-9ed0-7301256c09bd/GCF_022095695.1_ASM2209569v1_genomic.fna.gz --refList GCF_022095695.1_ASM2209569v1_genomic.fna/target_genomes.txt --output GCF_022095695.1_ASM2209569v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:41,808] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:41,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec894d93-04a3-482e-8cc3-44bb64a051d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:41,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec894d93-04a3-482e-8cc3-44bb64a051d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:41,822] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:41,823] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:41,823] [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
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	100.0	1256	1260	95	conclusive
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	78.1889	178	1260	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	78.031	184	1260	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	77.3642	97	1260	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.3069	148	1260	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.2574	139	1260	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	77.1111	133	1260	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	77.0927	134	1260	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.07	78	1260	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	77.0698	146	1260	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.061	146	1260	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	77.0377	74	1260	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.8755	124	1260	95	below_threshold
Gracilibacillus oryzae	strain=TD8	GCA_009498735.1	1672701	1672701	type	True	76.3598	67	1260	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.1568	53	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:41,825] [INFO] DFAST Taxonomy check result was written to GCF_022095695.1_ASM2209569v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:41,826] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:41,827] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:41,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec894d93-04a3-482e-8cc3-44bb64a051d8/dqc_reference/checkm_data
[2024-01-24 13:57:41,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:41,870] [INFO] Task started: CheckM
[2024-01-24 13:57:41,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022095695.1_ASM2209569v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022095695.1_ASM2209569v1_genomic.fna/checkm_input GCF_022095695.1_ASM2209569v1_genomic.fna/checkm_result
[2024-01-24 13:58:13,221] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:13,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:13,240] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:13,241] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:13,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022095695.1_ASM2209569v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:13,242] [INFO] Task started: Blastn
[2024-01-24 13:58:13,242] [INFO] Running command: blastn -query GCF_022095695.1_ASM2209569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec894d93-04a3-482e-8cc3-44bb64a051d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_022095695.1_ASM2209569v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:14,090] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:14,094] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:14,094] [INFO] Target genome list was writen to GCF_022095695.1_ASM2209569v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:14,104] [INFO] Task started: fastANI
[2024-01-24 13:58:14,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg87c2cb67-d740-485d-9ed0-7301256c09bd/GCF_022095695.1_ASM2209569v1_genomic.fna.gz --refList GCF_022095695.1_ASM2209569v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022095695.1_ASM2209569v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:26,316] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:26,331] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:26,332] [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_000612865.1	s__Virgibacillus picturae	95.3982	1077	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	conclusive
GCF_000724085.1	s__Virgibacillus manasiensis	84.7388	884	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_001310895.1	s__Virgibacillus halodenitrificans	78.1889	178	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	-
GCF_002287375.1	s__Virgibacillus_G profundi	78.0109	185	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_000725285.1	s__Virgibacillus sp000725285	77.8067	158	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_002266285.1	s__Virgibacillus_G indicus	77.6786	182	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.6002	141	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_900176885.1	s__Oceanobacillus senegalensis	77.3642	97	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_014638995.1	s__Virgibacillus_E oceani	77.2739	138	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	-
GCF_016909015.1	s__Gracilibacillus alcaliphilus	77.1457	54	1260	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_016908515.1	s__Virgibacillus_I halotolerans	77.0842	147	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018075365.1	s__Virgibacillus pantothenticus	77.0724	134	1260	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_000377765.1	s__Gracilibacillus lacisalsi	77.0707	73	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCF_001591585.1	s__Niallia circulans	76.213	54	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.18	98.58	0.93	0.91	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:26,333] [INFO] GTDB search result was written to GCF_022095695.1_ASM2209569v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:26,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:26,338] [INFO] DFAST_QC result json was written to GCF_022095695.1_ASM2209569v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:26,338] [INFO] DFAST_QC completed!
[2024-01-24 13:58:26,338] [INFO] Total running time: 0h1m10s