[2024-01-24 14:30:59,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,886] [INFO] DQC Reference Directory: /var/lib/cwl/stgf27e1cfa-dd33-4eb7-b0b4-372014cf5fa4/dqc_reference
[2024-01-24 14:31:01,201] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:01,201] [INFO] Task started: Prodigal
[2024-01-24 14:31:01,202] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e02e857-765b-4379-9158-e3b91ac13f23/GCF_007991655.1_ASM799165v1_genomic.fna.gz | prodigal -d GCF_007991655.1_ASM799165v1_genomic.fna/cds.fna -a GCF_007991655.1_ASM799165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:26,616] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:26,616] [INFO] Task started: HMMsearch
[2024-01-24 14:31:26,616] [INFO] Running command: hmmsearch --tblout GCF_007991655.1_ASM799165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf27e1cfa-dd33-4eb7-b0b4-372014cf5fa4/dqc_reference/reference_markers.hmm GCF_007991655.1_ASM799165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:27,026] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:27,027] [INFO] Found 6/6 markers.
[2024-01-24 14:31:27,074] [INFO] Query marker FASTA was written to GCF_007991655.1_ASM799165v1_genomic.fna/markers.fasta
[2024-01-24 14:31:27,075] [INFO] Task started: Blastn
[2024-01-24 14:31:27,075] [INFO] Running command: blastn -query GCF_007991655.1_ASM799165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf27e1cfa-dd33-4eb7-b0b4-372014cf5fa4/dqc_reference/reference_markers.fasta -out GCF_007991655.1_ASM799165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:27,725] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:27,728] [INFO] Selected 18 target genomes.
[2024-01-24 14:31:27,729] [INFO] Target genome list was writen to GCF_007991655.1_ASM799165v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:27,737] [INFO] Task started: fastANI
[2024-01-24 14:31:27,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e02e857-765b-4379-9158-e3b91ac13f23/GCF_007991655.1_ASM799165v1_genomic.fna.gz --refList GCF_007991655.1_ASM799165v1_genomic.fna/target_genomes.txt --output GCF_007991655.1_ASM799165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:40,939] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:40,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf27e1cfa-dd33-4eb7-b0b4-372014cf5fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:40,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf27e1cfa-dd33-4eb7-b0b4-372014cf5fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:40,946] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:40,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:40,947] [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
Segetibacter aerophilus	strain=NBRC 106135	GCA_007991655.1	670293	670293	type	True	100.0	1921	1926	95	conclusive
Segetibacter koreensis	strain=DSM 18137	GCA_000374045.1	398037	398037	type	True	77.0211	237	1926	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	76.0496	52	1926	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	75.9812	50	1926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:40,949] [INFO] DFAST Taxonomy check result was written to GCF_007991655.1_ASM799165v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:40,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:40,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:40,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf27e1cfa-dd33-4eb7-b0b4-372014cf5fa4/dqc_reference/checkm_data
[2024-01-24 14:31:40,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:41,011] [INFO] Task started: CheckM
[2024-01-24 14:31:41,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991655.1_ASM799165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991655.1_ASM799165v1_genomic.fna/checkm_input GCF_007991655.1_ASM799165v1_genomic.fna/checkm_result
[2024-01-24 14:32:49,120] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:49,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:49,151] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:49,151] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:49,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991655.1_ASM799165v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:49,154] [INFO] Task started: Blastn
[2024-01-24 14:32:49,154] [INFO] Running command: blastn -query GCF_007991655.1_ASM799165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf27e1cfa-dd33-4eb7-b0b4-372014cf5fa4/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991655.1_ASM799165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:50,106] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:50,110] [INFO] Selected 22 target genomes.
[2024-01-24 14:32:50,110] [INFO] Target genome list was writen to GCF_007991655.1_ASM799165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:50,129] [INFO] Task started: fastANI
[2024-01-24 14:32:50,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e02e857-765b-4379-9158-e3b91ac13f23/GCF_007991655.1_ASM799165v1_genomic.fna.gz --refList GCF_007991655.1_ASM799165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991655.1_ASM799165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:07,841] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:07,853] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:07,853] [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_007991655.1	s__Segetibacter aerophilus	100.0	1921	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000374045.1	s__Segetibacter koreensis	77.0327	235	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355875.1	s__Segetibacter sp017355875	76.9876	110	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050375.1	s__Segetibacter sp002050375	76.2583	142	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200915.1	s__AWTP1-9 sp016200915	76.1438	57	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	99.92	99.92	0.98	0.98	2	-
GCF_019130065.1	s__Parasegetibacter sp019130065	75.9812	50	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parasegetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268155.1	s__Ferruginibacter sp018268155	75.649	55	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:07,855] [INFO] GTDB search result was written to GCF_007991655.1_ASM799165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:07,855] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:07,858] [INFO] DFAST_QC result json was written to GCF_007991655.1_ASM799165v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:07,858] [INFO] DFAST_QC completed!
[2024-01-24 14:33:07,858] [INFO] Total running time: 0h2m8s