[2024-01-25 19:54:20,427] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:20,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:20,428] [INFO] DQC Reference Directory: /var/lib/cwl/stg321ed0d5-6149-43df-97e6-04139b8c9cb6/dqc_reference
[2024-01-25 19:54:21,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:21,595] [INFO] Task started: Prodigal
[2024-01-25 19:54:21,595] [INFO] Running command: gunzip -c /var/lib/cwl/stg90effbf3-d72f-4eb5-985a-b70637444ba1/GCF_000212735.1_ASM21273v1_genomic.fna.gz | prodigal -d GCF_000212735.1_ASM21273v1_genomic.fna/cds.fna -a GCF_000212735.1_ASM21273v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:10,610] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:10,610] [INFO] Task started: HMMsearch
[2024-01-25 19:55:10,610] [INFO] Running command: hmmsearch --tblout GCF_000212735.1_ASM21273v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg321ed0d5-6149-43df-97e6-04139b8c9cb6/dqc_reference/reference_markers.hmm GCF_000212735.1_ASM21273v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:11,143] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:11,144] [INFO] Found 6/6 markers.
[2024-01-25 19:55:11,210] [INFO] Query marker FASTA was written to GCF_000212735.1_ASM21273v1_genomic.fna/markers.fasta
[2024-01-25 19:55:11,210] [INFO] Task started: Blastn
[2024-01-25 19:55:11,210] [INFO] Running command: blastn -query GCF_000212735.1_ASM21273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg321ed0d5-6149-43df-97e6-04139b8c9cb6/dqc_reference/reference_markers.fasta -out GCF_000212735.1_ASM21273v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:11,764] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:11,767] [INFO] Selected 19 target genomes.
[2024-01-25 19:55:11,767] [INFO] Target genome list was writen to GCF_000212735.1_ASM21273v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:11,776] [INFO] Task started: fastANI
[2024-01-25 19:55:11,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg90effbf3-d72f-4eb5-985a-b70637444ba1/GCF_000212735.1_ASM21273v1_genomic.fna.gz --refList GCF_000212735.1_ASM21273v1_genomic.fna/target_genomes.txt --output GCF_000212735.1_ASM21273v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:33,366] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:33,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg321ed0d5-6149-43df-97e6-04139b8c9cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:33,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg321ed0d5-6149-43df-97e6-04139b8c9cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:33,371] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:33,372] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:33,372] [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
Haliscomenobacter hydrossis	strain=DSM 1100	GCA_000212735.1	2350	2350	type	True	100.0	2921	2921	95	conclusive
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	76.4846	53	2921	95	below_threshold
Flavilitoribacter nigricans	strain=NBRC 102662	GCA_002646595.1	70997	70997	type	True	75.4615	61	2921	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:33,373] [INFO] DFAST Taxonomy check result was written to GCF_000212735.1_ASM21273v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:33,374] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:33,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:33,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg321ed0d5-6149-43df-97e6-04139b8c9cb6/dqc_reference/checkm_data
[2024-01-25 19:55:33,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:33,455] [INFO] Task started: CheckM
[2024-01-25 19:55:33,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000212735.1_ASM21273v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000212735.1_ASM21273v1_genomic.fna/checkm_input GCF_000212735.1_ASM21273v1_genomic.fna/checkm_result
[2024-01-25 19:57:47,095] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:47,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:47,116] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:47,116] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:47,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000212735.1_ASM21273v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:47,118] [INFO] Task started: Blastn
[2024-01-25 19:57:47,118] [INFO] Running command: blastn -query GCF_000212735.1_ASM21273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg321ed0d5-6149-43df-97e6-04139b8c9cb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000212735.1_ASM21273v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:47,894] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:47,897] [INFO] Selected 19 target genomes.
[2024-01-25 19:57:47,897] [INFO] Target genome list was writen to GCF_000212735.1_ASM21273v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:47,915] [INFO] Task started: fastANI
[2024-01-25 19:57:47,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg90effbf3-d72f-4eb5-985a-b70637444ba1/GCF_000212735.1_ASM21273v1_genomic.fna.gz --refList GCF_000212735.1_ASM21273v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000212735.1_ASM21273v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:08,770] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:08,777] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:08,777] [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_000212735.1	s__Haliscomenobacter hydrossis	100.0	2921	2921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Haliscomenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016718685.1	s__Haliscomenobacter sp016718685	91.3487	1887	2921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Haliscomenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707205.1	s__JADJPL01 sp016707205	76.8174	80	2921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJPL01	95.0	98.92	98.80	0.91	0.90	3	-
GCA_013299105.1	s__Haliscomenobacter sp013299105	76.6406	347	2921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Haliscomenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002646595.1	s__Flavilitoribacter nigricans	75.4615	61	2921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Flavilitoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045895.1	s__Lewinella sp003045895	75.4233	68	2921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella	95.0	99.87	99.87	0.95	0.95	2	-
GCA_002344975.1	s__UBA2329 sp002344975	75.3887	76	2921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA2329	95.0	99.24	97.74	0.94	0.88	7	-
GCA_002698985.1	s__UBA6168 sp002698985	75.1537	53	2921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA6168	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321935.1	s__UBA6168 sp011321935	74.8473	54	2921	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA6168	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:08,778] [INFO] GTDB search result was written to GCF_000212735.1_ASM21273v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:08,779] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:08,797] [INFO] DFAST_QC result json was written to GCF_000212735.1_ASM21273v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:08,797] [INFO] DFAST_QC completed!
[2024-01-25 19:58:08,797] [INFO] Total running time: 0h3m48s