[2024-01-24 13:28:17,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:17,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:17,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f31d538-04a7-4912-b4dd-eb961f3f13c2/dqc_reference
[2024-01-24 13:28:18,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:18,681] [INFO] Task started: Prodigal
[2024-01-24 13:28:18,681] [INFO] Running command: gunzip -c /var/lib/cwl/stg0289c1fe-cc3e-4c33-b59a-b923c4b4c35a/GCF_000374485.1_ASM37448v1_genomic.fna.gz | prodigal -d GCF_000374485.1_ASM37448v1_genomic.fna/cds.fna -a GCF_000374485.1_ASM37448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:30,335] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:30,335] [INFO] Task started: HMMsearch
[2024-01-24 13:28:30,335] [INFO] Running command: hmmsearch --tblout GCF_000374485.1_ASM37448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f31d538-04a7-4912-b4dd-eb961f3f13c2/dqc_reference/reference_markers.hmm GCF_000374485.1_ASM37448v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:30,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:30,661] [INFO] Found 6/6 markers.
[2024-01-24 13:28:30,702] [INFO] Query marker FASTA was written to GCF_000374485.1_ASM37448v1_genomic.fna/markers.fasta
[2024-01-24 13:28:30,702] [INFO] Task started: Blastn
[2024-01-24 13:28:30,702] [INFO] Running command: blastn -query GCF_000374485.1_ASM37448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f31d538-04a7-4912-b4dd-eb961f3f13c2/dqc_reference/reference_markers.fasta -out GCF_000374485.1_ASM37448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:31,542] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:31,546] [INFO] Selected 30 target genomes.
[2024-01-24 13:28:31,546] [INFO] Target genome list was writen to GCF_000374485.1_ASM37448v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:31,564] [INFO] Task started: fastANI
[2024-01-24 13:28:31,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg0289c1fe-cc3e-4c33-b59a-b923c4b4c35a/GCF_000374485.1_ASM37448v1_genomic.fna.gz --refList GCF_000374485.1_ASM37448v1_genomic.fna/target_genomes.txt --output GCF_000374485.1_ASM37448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:56,081] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:56,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f31d538-04a7-4912-b4dd-eb961f3f13c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:56,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f31d538-04a7-4912-b4dd-eb961f3f13c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:56,088] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:56,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:56,089] [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
Algicola sagamiensis	strain=DSM 14643	GCA_000374485.1	163869	163869	type	True	100.0	1425	1429	95	conclusive
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	76.8571	50	1429	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	76.8566	50	1429	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	76.7173	52	1429	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	76.4777	54	1429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:56,090] [INFO] DFAST Taxonomy check result was written to GCF_000374485.1_ASM37448v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:56,091] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:56,091] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:56,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f31d538-04a7-4912-b4dd-eb961f3f13c2/dqc_reference/checkm_data
[2024-01-24 13:28:56,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:56,135] [INFO] Task started: CheckM
[2024-01-24 13:28:56,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000374485.1_ASM37448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000374485.1_ASM37448v1_genomic.fna/checkm_input GCF_000374485.1_ASM37448v1_genomic.fna/checkm_result
[2024-01-24 13:29:34,780] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:34,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:34,802] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:34,803] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:34,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000374485.1_ASM37448v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:34,804] [INFO] Task started: Blastn
[2024-01-24 13:29:34,804] [INFO] Running command: blastn -query GCF_000374485.1_ASM37448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f31d538-04a7-4912-b4dd-eb961f3f13c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000374485.1_ASM37448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:36,005] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:36,008] [INFO] Selected 27 target genomes.
[2024-01-24 13:29:36,008] [INFO] Target genome list was writen to GCF_000374485.1_ASM37448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:36,040] [INFO] Task started: fastANI
[2024-01-24 13:29:36,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg0289c1fe-cc3e-4c33-b59a-b923c4b4c35a/GCF_000374485.1_ASM37448v1_genomic.fna.gz --refList GCF_000374485.1_ASM37448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000374485.1_ASM37448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:57,422] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:57,433] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:57,434] [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_000374485.1	s__Algicola sagamiensis	100.0	1425	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Algicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000814765.1	s__Pseudoalteromonas luteoviolacea_H	77.236	53	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	95.23	95.23	0.92	0.92	2	-
GCF_001625695.1	s__Pseudoalteromonas luteoviolacea_B	77.1114	54	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.59	99.39	0.98	0.96	4	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	76.7491	51	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_001550155.1	s__Pseudoalteromonas arabiensis	76.4777	54	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:57,436] [INFO] GTDB search result was written to GCF_000374485.1_ASM37448v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:57,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:57,440] [INFO] DFAST_QC result json was written to GCF_000374485.1_ASM37448v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:57,440] [INFO] DFAST_QC completed!
[2024-01-24 13:29:57,440] [INFO] Total running time: 0h1m40s