[2024-01-24 13:32:13,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:13,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:13,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e91b6e1-638b-45db-9c85-55b43e17f565/dqc_reference
[2024-01-24 13:32:14,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:14,601] [INFO] Task started: Prodigal
[2024-01-24 13:32:14,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg1848e79c-fb87-4d10-a911-587756484b93/GCF_026001925.1_ASM2600192v1_genomic.fna.gz | prodigal -d GCF_026001925.1_ASM2600192v1_genomic.fna/cds.fna -a GCF_026001925.1_ASM2600192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:23,500] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:23,500] [INFO] Task started: HMMsearch
[2024-01-24 13:32:23,500] [INFO] Running command: hmmsearch --tblout GCF_026001925.1_ASM2600192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e91b6e1-638b-45db-9c85-55b43e17f565/dqc_reference/reference_markers.hmm GCF_026001925.1_ASM2600192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:23,756] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:23,757] [INFO] Found 6/6 markers.
[2024-01-24 13:32:23,790] [INFO] Query marker FASTA was written to GCF_026001925.1_ASM2600192v1_genomic.fna/markers.fasta
[2024-01-24 13:32:23,790] [INFO] Task started: Blastn
[2024-01-24 13:32:23,791] [INFO] Running command: blastn -query GCF_026001925.1_ASM2600192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e91b6e1-638b-45db-9c85-55b43e17f565/dqc_reference/reference_markers.fasta -out GCF_026001925.1_ASM2600192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:24,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:24,627] [INFO] Selected 14 target genomes.
[2024-01-24 13:32:24,627] [INFO] Target genome list was writen to GCF_026001925.1_ASM2600192v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:24,643] [INFO] Task started: fastANI
[2024-01-24 13:32:24,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg1848e79c-fb87-4d10-a911-587756484b93/GCF_026001925.1_ASM2600192v1_genomic.fna.gz --refList GCF_026001925.1_ASM2600192v1_genomic.fna/target_genomes.txt --output GCF_026001925.1_ASM2600192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:36,450] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:36,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e91b6e1-638b-45db-9c85-55b43e17f565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:36,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e91b6e1-638b-45db-9c85-55b43e17f565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:36,469] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:36,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:36,470] [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
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	99.9748	1176	1221	95	conclusive
Vibrio aphrogenes	strain=CA-1004	GCA_002157735.2	1891186	1891186	type	True	81.8834	654	1221	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	81.6734	666	1221	95	below_threshold
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	81.3332	674	1221	95	below_threshold
Vibrio litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	81.219	665	1221	95	below_threshold
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	80.4015	549	1221	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	79.8049	423	1221	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.5291	227	1221	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.4863	257	1221	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	79.4846	249	1221	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	79.2871	224	1221	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	79.2554	229	1221	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	78.7401	233	1221	95	below_threshold
Aliivibrio finisterrensis	strain=LMG 23869	GCA_008933155.1	511998	511998	suspected-type	True	78.4095	193	1221	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:36,472] [INFO] DFAST Taxonomy check result was written to GCF_026001925.1_ASM2600192v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:36,472] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:36,472] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:36,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e91b6e1-638b-45db-9c85-55b43e17f565/dqc_reference/checkm_data
[2024-01-24 13:32:36,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:36,511] [INFO] Task started: CheckM
[2024-01-24 13:32:36,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026001925.1_ASM2600192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026001925.1_ASM2600192v1_genomic.fna/checkm_input GCF_026001925.1_ASM2600192v1_genomic.fna/checkm_result
[2024-01-24 13:33:10,370] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:10,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,388] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:10,389] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:10,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026001925.1_ASM2600192v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:10,390] [INFO] Task started: Blastn
[2024-01-24 13:33:10,390] [INFO] Running command: blastn -query GCF_026001925.1_ASM2600192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e91b6e1-638b-45db-9c85-55b43e17f565/dqc_reference/reference_markers_gtdb.fasta -out GCF_026001925.1_ASM2600192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:11,799] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:11,802] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:11,803] [INFO] Target genome list was writen to GCF_026001925.1_ASM2600192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:11,817] [INFO] Task started: fastANI
[2024-01-24 13:33:11,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg1848e79c-fb87-4d10-a911-587756484b93/GCF_026001925.1_ASM2600192v1_genomic.fna.gz --refList GCF_026001925.1_ASM2600192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026001925.1_ASM2600192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:21,049] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:21,058] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:21,058] [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_002934045.1	s__Vibrio gangliei	99.9748	1176	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002157735.2	s__Vibrio aphrogenes	81.8475	661	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218005.2	s__Vibrio algivorus	81.6739	664	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.65	98.65	0.88	0.88	2	-
GCF_002218045.2	s__Vibrio rumoiensis	81.308	674	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426765.1	s__Vibrio litoralis	81.2281	663	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	-
GCF_002218025.2	s__Vibrio casei	80.3917	551	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.63	99.33	0.95	0.89	5	-
GCF_000286955.2	s__Vibrio rumoiensis_A	79.9952	508	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601765.2	s__Vibrio sp009601765	79.7873	422	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.01	99.01	0.85	0.85	2	-
GCF_000827885.1	s__Vibrio renipiscarius	78.731	231	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008933155.1	s__Aliivibrio finisterrensis	78.4085	193	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	95.53	95.03	0.81	0.80	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:21,060] [INFO] GTDB search result was written to GCF_026001925.1_ASM2600192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:21,060] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:21,064] [INFO] DFAST_QC result json was written to GCF_026001925.1_ASM2600192v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:21,064] [INFO] DFAST_QC completed!
[2024-01-24 13:33:21,064] [INFO] Total running time: 0h1m8s