[2024-01-24 14:30:45,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:45,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:45,055] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7800269-b9ce-4c42-b199-5ecbf2f45f71/dqc_reference
[2024-01-24 14:30:46,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:46,480] [INFO] Task started: Prodigal
[2024-01-24 14:30:46,480] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8fc2522-3cee-4141-acce-0476697c7ab7/GCF_000956595.1_ASM95659v1_genomic.fna.gz | prodigal -d GCF_000956595.1_ASM95659v1_genomic.fna/cds.fna -a GCF_000956595.1_ASM95659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:56,816] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:56,816] [INFO] Task started: HMMsearch
[2024-01-24 14:30:56,816] [INFO] Running command: hmmsearch --tblout GCF_000956595.1_ASM95659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7800269-b9ce-4c42-b199-5ecbf2f45f71/dqc_reference/reference_markers.hmm GCF_000956595.1_ASM95659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:57,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:57,189] [INFO] Found 6/6 markers.
[2024-01-24 14:30:57,240] [INFO] Query marker FASTA was written to GCF_000956595.1_ASM95659v1_genomic.fna/markers.fasta
[2024-01-24 14:30:57,240] [INFO] Task started: Blastn
[2024-01-24 14:30:57,241] [INFO] Running command: blastn -query GCF_000956595.1_ASM95659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7800269-b9ce-4c42-b199-5ecbf2f45f71/dqc_reference/reference_markers.fasta -out GCF_000956595.1_ASM95659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:57,977] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:57,980] [INFO] Selected 14 target genomes.
[2024-01-24 14:30:57,980] [INFO] Target genome list was writen to GCF_000956595.1_ASM95659v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:57,986] [INFO] Task started: fastANI
[2024-01-24 14:30:57,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8fc2522-3cee-4141-acce-0476697c7ab7/GCF_000956595.1_ASM95659v1_genomic.fna.gz --refList GCF_000956595.1_ASM95659v1_genomic.fna/target_genomes.txt --output GCF_000956595.1_ASM95659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:12,500] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:12,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7800269-b9ce-4c42-b199-5ecbf2f45f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:12,501] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7800269-b9ce-4c42-b199-5ecbf2f45f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:12,513] [INFO] Found 14 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 14:31:12,513] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:31:12,513] [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
Priestia aryabhattai	strain=B8W22	GCA_000956595.1	412384	412384	type	True	100.0	1659	1665	95	inconclusive
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	95.5499	1524	1665	95	inconclusive
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	95.5348	1509	1665	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_000832985.1	1404	1404	type	True	95.5311	1513	1665	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	95.5076	1538	1665	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_006094495.1	1404	1404	type	True	95.4968	1527	1665	95	inconclusive
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	77.1053	89	1665	95	below_threshold
Mangrovibacillus cuniculi	strain=R1DC41	GCA_015482585.1	2593652	2593652	type	True	77.0095	70	1665	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.9094	99	1665	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.8219	87	1665	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.7635	105	1665	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	76.7518	97	1665	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.5086	109	1665	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	76.212	80	1665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:12,515] [INFO] DFAST Taxonomy check result was written to GCF_000956595.1_ASM95659v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:12,516] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:12,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:12,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7800269-b9ce-4c42-b199-5ecbf2f45f71/dqc_reference/checkm_data
[2024-01-24 14:31:12,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:12,572] [INFO] Task started: CheckM
[2024-01-24 14:31:12,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000956595.1_ASM95659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000956595.1_ASM95659v1_genomic.fna/checkm_input GCF_000956595.1_ASM95659v1_genomic.fna/checkm_result
[2024-01-24 14:31:48,597] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:48,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:48,623] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:48,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:48,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000956595.1_ASM95659v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:48,624] [INFO] Task started: Blastn
[2024-01-24 14:31:48,624] [INFO] Running command: blastn -query GCF_000956595.1_ASM95659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7800269-b9ce-4c42-b199-5ecbf2f45f71/dqc_reference/reference_markers_gtdb.fasta -out GCF_000956595.1_ASM95659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:49,489] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:49,493] [INFO] Selected 12 target genomes.
[2024-01-24 14:31:49,493] [INFO] Target genome list was writen to GCF_000956595.1_ASM95659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:49,505] [INFO] Task started: fastANI
[2024-01-24 14:31:49,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8fc2522-3cee-4141-acce-0476697c7ab7/GCF_000956595.1_ASM95659v1_genomic.fna.gz --refList GCF_000956595.1_ASM95659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000956595.1_ASM95659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:00,785] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:00,799] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:00,799] [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_000956595.1	s__Priestia aryabhattai	100.0	1659	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	96.022	97.07	96.58	0.92	0.91	12	conclusive
GCF_009497655.1	s__Priestia megaterium_A	96.022	1486	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	96.022	98.08	96.36	0.92	0.89	34	conclusive
GCF_000832985.1	s__Priestia megaterium	95.5187	1514	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.5311	96.82	95.69	0.88	0.73	151	-
GCF_008180335.1	s__Priestia megaterium_B	79.8662	500	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591565.1	s__Priestia flexa	79.3043	407	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
GCF_002265635.1	s__Priestia aryabhattai_A	79.2197	426	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	98.53	98.16	0.94	0.93	4	-
GCF_016909075.1	s__Priestia iocasae	78.487	274	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274935.1	s__Bacillus_AG koreensis	77.852	204	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013200995.1	s__Gottfriedia sp002556365	76.8868	91	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	95.58	95.58	0.84	0.83	3	-
GCA_001938995.1	s__Bacillus pumilus_G	76.8837	79	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002577655.1	s__Metabacillus sp002577655	76.8646	118	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509555.1	s__Cytobacillus sp001509555	76.4039	89	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:00,801] [INFO] GTDB search result was written to GCF_000956595.1_ASM95659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:00,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:00,807] [INFO] DFAST_QC result json was written to GCF_000956595.1_ASM95659v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:00,807] [INFO] DFAST_QC completed!
[2024-01-24 14:32:00,807] [INFO] Total running time: 0h1m16s