[2024-01-24 12:36:55,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:55,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:55,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg39973fe0-256a-48cb-a5be-5fdd69d45009/dqc_reference
[2024-01-24 12:36:57,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:57,085] [INFO] Task started: Prodigal
[2024-01-24 12:36:57,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ac6d915-f9c3-45a1-9136-e974642e5ae8/GCF_020734105.1_ASM2073410v1_genomic.fna.gz | prodigal -d GCF_020734105.1_ASM2073410v1_genomic.fna/cds.fna -a GCF_020734105.1_ASM2073410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:07,264] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:07,264] [INFO] Task started: HMMsearch
[2024-01-24 12:37:07,264] [INFO] Running command: hmmsearch --tblout GCF_020734105.1_ASM2073410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39973fe0-256a-48cb-a5be-5fdd69d45009/dqc_reference/reference_markers.hmm GCF_020734105.1_ASM2073410v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:07,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:07,642] [INFO] Found 6/6 markers.
[2024-01-24 12:37:07,690] [INFO] Query marker FASTA was written to GCF_020734105.1_ASM2073410v1_genomic.fna/markers.fasta
[2024-01-24 12:37:07,691] [INFO] Task started: Blastn
[2024-01-24 12:37:07,691] [INFO] Running command: blastn -query GCF_020734105.1_ASM2073410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39973fe0-256a-48cb-a5be-5fdd69d45009/dqc_reference/reference_markers.fasta -out GCF_020734105.1_ASM2073410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:08,276] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:08,280] [INFO] Selected 18 target genomes.
[2024-01-24 12:37:08,280] [INFO] Target genome list was writen to GCF_020734105.1_ASM2073410v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:08,298] [INFO] Task started: fastANI
[2024-01-24 12:37:08,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac6d915-f9c3-45a1-9136-e974642e5ae8/GCF_020734105.1_ASM2073410v1_genomic.fna.gz --refList GCF_020734105.1_ASM2073410v1_genomic.fna/target_genomes.txt --output GCF_020734105.1_ASM2073410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:20,775] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:20,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39973fe0-256a-48cb-a5be-5fdd69d45009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:20,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39973fe0-256a-48cb-a5be-5fdd69d45009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:20,787] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:20,787] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:20,787] [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 akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	79.5859	501	1642	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	79.5844	502	1642	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	79.4399	513	1642	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	79.4263	503	1642	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	78.8865	415	1642	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	78.4777	366	1642	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	78.4665	367	1642	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	78.3394	239	1642	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	78.2676	276	1642	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_001315065.1	127886	127886	type	True	77.4776	175	1642	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.1841	68	1642	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	77.0505	141	1642	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	76.9494	100	1642	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.7068	128	1642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:20,789] [INFO] DFAST Taxonomy check result was written to GCF_020734105.1_ASM2073410v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:20,789] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:20,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:20,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39973fe0-256a-48cb-a5be-5fdd69d45009/dqc_reference/checkm_data
[2024-01-24 12:37:20,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:20,851] [INFO] Task started: CheckM
[2024-01-24 12:37:20,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020734105.1_ASM2073410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020734105.1_ASM2073410v1_genomic.fna/checkm_input GCF_020734105.1_ASM2073410v1_genomic.fna/checkm_result
[2024-01-24 12:37:56,516] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:56,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:56,537] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:56,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:56,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020734105.1_ASM2073410v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:56,538] [INFO] Task started: Blastn
[2024-01-24 12:37:56,538] [INFO] Running command: blastn -query GCF_020734105.1_ASM2073410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39973fe0-256a-48cb-a5be-5fdd69d45009/dqc_reference/reference_markers_gtdb.fasta -out GCF_020734105.1_ASM2073410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:57,366] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:57,369] [INFO] Selected 18 target genomes.
[2024-01-24 12:37:57,370] [INFO] Target genome list was writen to GCF_020734105.1_ASM2073410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:57,389] [INFO] Task started: fastANI
[2024-01-24 12:37:57,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac6d915-f9c3-45a1-9136-e974642e5ae8/GCF_020734105.1_ASM2073410v1_genomic.fna.gz --refList GCF_020734105.1_ASM2073410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020734105.1_ASM2073410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:10,211] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:10,232] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:38:10,232] [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_000513135.1	s__Bacillus_L akibai	79.5841	502	1642	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_002109385.1	s__Bacillus_L krulwichiae	79.4497	512	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002797395.1	s__45385 sp002797395	78.9573	267	1642	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_000787375.1	s__Bacillus_L okhensis	78.8816	415	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513095.1	s__Bacillus_L wakoensis	78.4814	365	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017939705.1	s__Bacillus_L sp017939705	78.3616	240	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	78.2865	276	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156385.1	s__45385 sp002156385	78.2213	229	1642	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_000005825.2	s__Bacillus_S pseudofirmus	77.9758	175	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	77.4955	174	1642	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_001866005.1	s__Anaerobacillus alkalilacustris	77.4821	107	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590835.1	s__Bacillus_A gaemokensis	77.2648	60	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_016798245.1	s__Alkalihalobacillus_A gibsonii_A	77.0335	86	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	77.0145	140	1642	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_001865995.1	s__Anaerobacillus arseniciselenatis	76.9751	99	1642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:10,235] [INFO] GTDB search result was written to GCF_020734105.1_ASM2073410v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:10,235] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:10,239] [INFO] DFAST_QC result json was written to GCF_020734105.1_ASM2073410v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:10,240] [INFO] DFAST_QC completed!
[2024-01-24 12:38:10,240] [INFO] Total running time: 0h1m15s