[2024-01-24 11:05:49,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,407] [INFO] DQC Reference Directory: /var/lib/cwl/stgef8f7274-96c3-4b92-b702-bb9cc101ff92/dqc_reference
[2024-01-24 11:05:51,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,279] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,280] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e239652-7315-4882-9ee5-13dfa6b54ece/GCF_001038425.2_ASM103842v2_genomic.fna.gz | prodigal -d GCF_001038425.2_ASM103842v2_genomic.fna/cds.fna -a GCF_001038425.2_ASM103842v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:57,851] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:57,851] [INFO] Task started: HMMsearch
[2024-01-24 11:05:57,851] [INFO] Running command: hmmsearch --tblout GCF_001038425.2_ASM103842v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef8f7274-96c3-4b92-b702-bb9cc101ff92/dqc_reference/reference_markers.hmm GCF_001038425.2_ASM103842v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:58,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:58,075] [INFO] Found 6/6 markers.
[2024-01-24 11:05:58,101] [INFO] Query marker FASTA was written to GCF_001038425.2_ASM103842v2_genomic.fna/markers.fasta
[2024-01-24 11:05:58,101] [INFO] Task started: Blastn
[2024-01-24 11:05:58,101] [INFO] Running command: blastn -query GCF_001038425.2_ASM103842v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgef8f7274-96c3-4b92-b702-bb9cc101ff92/dqc_reference/reference_markers.fasta -out GCF_001038425.2_ASM103842v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:59,299] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:59,302] [INFO] Selected 24 target genomes.
[2024-01-24 11:05:59,303] [INFO] Target genome list was writen to GCF_001038425.2_ASM103842v2_genomic.fna/target_genomes.txt
[2024-01-24 11:05:59,374] [INFO] Task started: fastANI
[2024-01-24 11:05:59,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e239652-7315-4882-9ee5-13dfa6b54ece/GCF_001038425.2_ASM103842v2_genomic.fna.gz --refList GCF_001038425.2_ASM103842v2_genomic.fna/target_genomes.txt --output GCF_001038425.2_ASM103842v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:12,424] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:12,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef8f7274-96c3-4b92-b702-bb9cc101ff92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:12,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef8f7274-96c3-4b92-b702-bb9cc101ff92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:12,436] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:12,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:12,436] [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
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	100.0	1099	1104	95	conclusive
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	78.6301	335	1104	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	78.4247	311	1104	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	78.2305	295	1104	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.8578	175	1104	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	77.6945	112	1104	95	below_threshold
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	77.6385	96	1104	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.4775	164	1104	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	77.3876	83	1104	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	77.1781	127	1104	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	77.0815	62	1104	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	76.9505	137	1104	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	76.6598	51	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:12,437] [INFO] DFAST Taxonomy check result was written to GCF_001038425.2_ASM103842v2_genomic.fna/tc_result.tsv
[2024-01-24 11:06:12,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:12,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:12,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef8f7274-96c3-4b92-b702-bb9cc101ff92/dqc_reference/checkm_data
[2024-01-24 11:06:12,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:12,471] [INFO] Task started: CheckM
[2024-01-24 11:06:12,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001038425.2_ASM103842v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001038425.2_ASM103842v2_genomic.fna/checkm_input GCF_001038425.2_ASM103842v2_genomic.fna/checkm_result
[2024-01-24 11:06:37,117] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:37,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:37,142] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:37,142] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:37,143] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001038425.2_ASM103842v2_genomic.fna/markers.fasta)
[2024-01-24 11:06:37,143] [INFO] Task started: Blastn
[2024-01-24 11:06:37,143] [INFO] Running command: blastn -query GCF_001038425.2_ASM103842v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgef8f7274-96c3-4b92-b702-bb9cc101ff92/dqc_reference/reference_markers_gtdb.fasta -out GCF_001038425.2_ASM103842v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:37,896] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:37,899] [INFO] Selected 18 target genomes.
[2024-01-24 11:06:37,899] [INFO] Target genome list was writen to GCF_001038425.2_ASM103842v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:37,926] [INFO] Task started: fastANI
[2024-01-24 11:06:37,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e239652-7315-4882-9ee5-13dfa6b54ece/GCF_001038425.2_ASM103842v2_genomic.fna.gz --refList GCF_001038425.2_ASM103842v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001038425.2_ASM103842v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:50,277] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:50,290] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:50,290] [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_001038425.2	s__Ornithinibacillus contaminans	100.0	1099	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001038485.1	s__Ornithinibacillus californiensis	79.7579	352	1104	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_018310345.1	s__Ornithinibacillus massiliensis	78.6301	335	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	99.20	99.20	0.97	0.97	2	-
GCF_000577245.1	s__Ornithinibacillus sp000577245	78.4947	336	1104	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_000190475.1	s__Ornithinibacillus scapharcae	78.4247	311	1104	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_900184735.1	s__Ornithinibacillus globulus_B	78.4098	329	1104	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_000482485.1	s__Ornithinibacillus globulus	78.366	339	1104	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_014637405.1	s__Ornithinibacillus halotolerans	78.2435	294	1104	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_009728145.1	s__Ornithinibacillus caprae	77.8749	223	1104	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_900129485.1	s__Ornithinibacillus halophilus	77.8578	175	1104	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_003665065.1	s__Oceanobacillus piezotolerans	77.6385	96	1104	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_001618145.1	s__Oceanobacillus damuensis	77.3876	83	1104	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_007679095.1	s__DE0126 sp007679095	77.1854	52	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003400205.1	s__Fredinandcohnia sp003400205	76.8219	72	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799755.1	s__Fredinandcohnia timonensis_A	76.7565	73	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	76.5638	72	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:50,292] [INFO] GTDB search result was written to GCF_001038425.2_ASM103842v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:50,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:50,297] [INFO] DFAST_QC result json was written to GCF_001038425.2_ASM103842v2_genomic.fna/dqc_result.json
[2024-01-24 11:06:50,297] [INFO] DFAST_QC completed!
[2024-01-24 11:06:50,297] [INFO] Total running time: 0h1m1s