[2024-01-24 11:52:49,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:49,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:49,891] [INFO] DQC Reference Directory: /var/lib/cwl/stgce6a45b9-f6f8-45ea-b473-8713743c8b11/dqc_reference
[2024-01-24 11:52:51,107] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:51,107] [INFO] Task started: Prodigal
[2024-01-24 11:52:51,108] [INFO] Running command: gunzip -c /var/lib/cwl/stg9463bbef-fe7d-4fdb-b262-de7ad41b3bda/GCF_001592025.1_ASM159202v1_genomic.fna.gz | prodigal -d GCF_001592025.1_ASM159202v1_genomic.fna/cds.fna -a GCF_001592025.1_ASM159202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:57,817] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:57,818] [INFO] Task started: HMMsearch
[2024-01-24 11:52:57,818] [INFO] Running command: hmmsearch --tblout GCF_001592025.1_ASM159202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce6a45b9-f6f8-45ea-b473-8713743c8b11/dqc_reference/reference_markers.hmm GCF_001592025.1_ASM159202v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:58,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:58,104] [INFO] Found 6/6 markers.
[2024-01-24 11:52:58,156] [INFO] Query marker FASTA was written to GCF_001592025.1_ASM159202v1_genomic.fna/markers.fasta
[2024-01-24 11:52:58,157] [INFO] Task started: Blastn
[2024-01-24 11:52:58,157] [INFO] Running command: blastn -query GCF_001592025.1_ASM159202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce6a45b9-f6f8-45ea-b473-8713743c8b11/dqc_reference/reference_markers.fasta -out GCF_001592025.1_ASM159202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:58,747] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:58,751] [INFO] Selected 26 target genomes.
[2024-01-24 11:52:58,752] [INFO] Target genome list was writen to GCF_001592025.1_ASM159202v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:58,792] [INFO] Task started: fastANI
[2024-01-24 11:52:58,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg9463bbef-fe7d-4fdb-b262-de7ad41b3bda/GCF_001592025.1_ASM159202v1_genomic.fna.gz --refList GCF_001592025.1_ASM159202v1_genomic.fna/target_genomes.txt --output GCF_001592025.1_ASM159202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:13,346] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:13,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce6a45b9-f6f8-45ea-b473-8713743c8b11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:13,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce6a45b9-f6f8-45ea-b473-8713743c8b11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:13,365] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:53:13,365] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:53:13,366] [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
Alkalihalobacillus trypoxylicola	strain=NBRC 102646	GCA_001592025.1	519424	519424	type	True	100.0	1252	1266	95	conclusive
Alkalihalobacillus trypoxylicola	strain=KCTC 13244	GCA_001590785.1	519424	519424	type	True	99.9955	1266	1266	95	conclusive
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	78.149	264	1266	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	78.1109	246	1266	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	77.2492	104	1266	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	77.1237	116	1266	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	77.1028	117	1266	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.9328	102	1266	95	below_threshold
Halalkalibacterium ligniniphilum	strain=L1	GCA_000334155.1	1134413	1134413	type	True	76.8899	95	1266	95	below_threshold
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	76.2587	83	1266	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	75.7882	53	1266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:13,367] [INFO] DFAST Taxonomy check result was written to GCF_001592025.1_ASM159202v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:13,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:13,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:13,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce6a45b9-f6f8-45ea-b473-8713743c8b11/dqc_reference/checkm_data
[2024-01-24 11:53:13,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:13,410] [INFO] Task started: CheckM
[2024-01-24 11:53:13,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592025.1_ASM159202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592025.1_ASM159202v1_genomic.fna/checkm_input GCF_001592025.1_ASM159202v1_genomic.fna/checkm_result
[2024-01-24 11:53:39,935] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:39,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:39,962] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:39,963] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:39,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592025.1_ASM159202v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:39,963] [INFO] Task started: Blastn
[2024-01-24 11:53:39,964] [INFO] Running command: blastn -query GCF_001592025.1_ASM159202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce6a45b9-f6f8-45ea-b473-8713743c8b11/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592025.1_ASM159202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:40,807] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:40,811] [INFO] Selected 25 target genomes.
[2024-01-24 11:53:40,811] [INFO] Target genome list was writen to GCF_001592025.1_ASM159202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:40,859] [INFO] Task started: fastANI
[2024-01-24 11:53:40,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg9463bbef-fe7d-4fdb-b262-de7ad41b3bda/GCF_001592025.1_ASM159202v1_genomic.fna.gz --refList GCF_001592025.1_ASM159202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592025.1_ASM159202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:55,510] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:55,524] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:55,524] [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_001590785.1	s__Alkalihalobacillus trypoxylicola	99.9955	1266	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	98.48	96.97	0.95	0.90	3	conclusive
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	78.2364	238	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	78.1632	263	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_002797395.1	s__45385 sp002797395	77.6358	98	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621445.1	s__Bacillus_AO bogoriensis	77.2532	103	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797325.1	s__Bacillus_S sp002797325	77.1922	93	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513135.1	s__Bacillus_L akibai	77.0866	116	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	77.0526	97	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000474275.2	s__Bacillus_S marmarensis	76.9334	101	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
GCF_000334155.1	s__Bacillus_AN ligniniphilus	76.9132	94	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_AN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019795.1	s__Bacillus_AO alkalicellulosilyticus	76.2516	82	1266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:55,526] [INFO] GTDB search result was written to GCF_001592025.1_ASM159202v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:55,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:55,530] [INFO] DFAST_QC result json was written to GCF_001592025.1_ASM159202v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:55,530] [INFO] DFAST_QC completed!
[2024-01-24 11:53:55,530] [INFO] Total running time: 0h1m6s