[2024-01-24 13:57:13,508] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg575399d5-16fc-432c-a2f9-7ac6462b7303/dqc_reference
[2024-01-24 13:57:14,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,954] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,955] [INFO] Running command: gunzip -c /var/lib/cwl/stg40a4dd87-3cde-46c2-927a-72995feb3a93/GCF_003545695.1_ASM354569v1_genomic.fna.gz | prodigal -d GCF_003545695.1_ASM354569v1_genomic.fna/cds.fna -a GCF_003545695.1_ASM354569v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:39,494] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:39,494] [INFO] Task started: HMMsearch
[2024-01-24 13:57:39,494] [INFO] Running command: hmmsearch --tblout GCF_003545695.1_ASM354569v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg575399d5-16fc-432c-a2f9-7ac6462b7303/dqc_reference/reference_markers.hmm GCF_003545695.1_ASM354569v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:39,832] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:39,834] [INFO] Found 6/6 markers.
[2024-01-24 13:57:39,875] [INFO] Query marker FASTA was written to GCF_003545695.1_ASM354569v1_genomic.fna/markers.fasta
[2024-01-24 13:57:39,876] [INFO] Task started: Blastn
[2024-01-24 13:57:39,876] [INFO] Running command: blastn -query GCF_003545695.1_ASM354569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg575399d5-16fc-432c-a2f9-7ac6462b7303/dqc_reference/reference_markers.fasta -out GCF_003545695.1_ASM354569v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:40,481] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:40,484] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:40,485] [INFO] Target genome list was writen to GCF_003545695.1_ASM354569v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:40,489] [INFO] Task started: fastANI
[2024-01-24 13:57:40,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg40a4dd87-3cde-46c2-927a-72995feb3a93/GCF_003545695.1_ASM354569v1_genomic.fna.gz --refList GCF_003545695.1_ASM354569v1_genomic.fna/target_genomes.txt --output GCF_003545695.1_ASM354569v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:56,284] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:56,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg575399d5-16fc-432c-a2f9-7ac6462b7303/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:56,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg575399d5-16fc-432c-a2f9-7ac6462b7303/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:56,296] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:56,297] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:56,297] [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
Taibaiella helva	strain=F-4	GCA_003545695.1	2301235	2301235	type	True	100.0	1592	1592	95	conclusive
Taibaiella koreensis	strain=THG-DT86	GCA_003545715.1	1268548	1268548	type	True	81.3525	1095	1592	95	below_threshold
Taibaiella chishuiensis	strain=CGMCC 1.12700	GCA_003014535.1	1434707	1434707	type	True	77.5907	408	1592	95	below_threshold
Taibaiella lutea	strain=KVB11	GCA_008629695.1	2608001	2608001	type	True	77.1191	132	1592	95	below_threshold
Terrimonas ferruginea	strain=DSM 30193	GCA_000425585.1	249	249	type	True	76.2071	53	1592	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	76.1163	60	1592	95	below_threshold
Chitinophaga japonensis	strain=DSM 13484	GCA_007830125.1	104662	104662	type	True	76.047	101	1592	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	75.8421	92	1592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:56,303] [INFO] DFAST Taxonomy check result was written to GCF_003545695.1_ASM354569v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:56,304] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:56,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:56,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg575399d5-16fc-432c-a2f9-7ac6462b7303/dqc_reference/checkm_data
[2024-01-24 13:57:56,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:56,364] [INFO] Task started: CheckM
[2024-01-24 13:57:56,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003545695.1_ASM354569v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003545695.1_ASM354569v1_genomic.fna/checkm_input GCF_003545695.1_ASM354569v1_genomic.fna/checkm_result
[2024-01-24 13:59:05,946] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:05,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:05,969] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:05,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003545695.1_ASM354569v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:05,970] [INFO] Task started: Blastn
[2024-01-24 13:59:05,970] [INFO] Running command: blastn -query GCF_003545695.1_ASM354569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg575399d5-16fc-432c-a2f9-7ac6462b7303/dqc_reference/reference_markers_gtdb.fasta -out GCF_003545695.1_ASM354569v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:06,959] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:06,963] [INFO] Selected 17 target genomes.
[2024-01-24 13:59:06,963] [INFO] Target genome list was writen to GCF_003545695.1_ASM354569v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:06,972] [INFO] Task started: fastANI
[2024-01-24 13:59:06,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg40a4dd87-3cde-46c2-927a-72995feb3a93/GCF_003545695.1_ASM354569v1_genomic.fna.gz --refList GCF_003545695.1_ASM354569v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003545695.1_ASM354569v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:19,903] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:19,915] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:19,915] [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_003545695.1	s__Edaphocola helva	100.0	1592	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003545715.1	s__Edaphocola koreensis	81.3487	1096	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014535.1	s__Edaphocola chishuiensis	77.5981	407	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629695.1	s__Edaphocola lutea	77.1216	131	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897835.1	s__Flavipsychrobacter sp001897835	76.5276	58	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897155.1	s__Edaphocola sp001897155	76.3302	82	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267955.1	s__Flavipsychrobacter sp018267955	76.1605	51	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786525.1	s__UBA1312 sp016786525	76.0434	105	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA1312	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786705.1	s__Edaphocola sp016786705	75.9157	81	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:19,917] [INFO] GTDB search result was written to GCF_003545695.1_ASM354569v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:19,917] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:19,920] [INFO] DFAST_QC result json was written to GCF_003545695.1_ASM354569v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:19,921] [INFO] DFAST_QC completed!
[2024-01-24 13:59:19,921] [INFO] Total running time: 0h2m6s