[2024-01-25 19:11:50,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:50,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:50,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ef8e73c-3282-494c-90d0-7faaaa12bc49/dqc_reference
[2024-01-25 19:11:51,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:51,841] [INFO] Task started: Prodigal
[2024-01-25 19:11:51,841] [INFO] Running command: gunzip -c /var/lib/cwl/stge7cf0188-bea4-4431-84b5-6af43dc79be2/GCF_021655555.1_ASM2165555v1_genomic.fna.gz | prodigal -d GCF_021655555.1_ASM2165555v1_genomic.fna/cds.fna -a GCF_021655555.1_ASM2165555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:03,594] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:03,595] [INFO] Task started: HMMsearch
[2024-01-25 19:12:03,595] [INFO] Running command: hmmsearch --tblout GCF_021655555.1_ASM2165555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ef8e73c-3282-494c-90d0-7faaaa12bc49/dqc_reference/reference_markers.hmm GCF_021655555.1_ASM2165555v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:03,888] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:03,889] [INFO] Found 6/6 markers.
[2024-01-25 19:12:03,931] [INFO] Query marker FASTA was written to GCF_021655555.1_ASM2165555v1_genomic.fna/markers.fasta
[2024-01-25 19:12:03,931] [INFO] Task started: Blastn
[2024-01-25 19:12:03,931] [INFO] Running command: blastn -query GCF_021655555.1_ASM2165555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ef8e73c-3282-494c-90d0-7faaaa12bc49/dqc_reference/reference_markers.fasta -out GCF_021655555.1_ASM2165555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:04,575] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:04,579] [INFO] Selected 32 target genomes.
[2024-01-25 19:12:04,579] [INFO] Target genome list was writen to GCF_021655555.1_ASM2165555v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:04,593] [INFO] Task started: fastANI
[2024-01-25 19:12:04,594] [INFO] Running command: fastANI --query /var/lib/cwl/stge7cf0188-bea4-4431-84b5-6af43dc79be2/GCF_021655555.1_ASM2165555v1_genomic.fna.gz --refList GCF_021655555.1_ASM2165555v1_genomic.fna/target_genomes.txt --output GCF_021655555.1_ASM2165555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:23,856] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:23,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ef8e73c-3282-494c-90d0-7faaaa12bc49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:23,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ef8e73c-3282-494c-90d0-7faaaa12bc49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:23,864] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:12:23,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:12:23,864] [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
Teredinibacter haidensis	strain=Bs08	GCA_014211975.1	2731755	2731755	type	True	80.0178	70	1770	95	below_threshold
Marinagarivorans algicola	strain=Z1	GCA_001292705.1	1513270	1513270	type	True	78.2407	239	1770	95	below_threshold
Teredinibacter purpureus	strain=Bs12	GCA_000966245.1	2731756	2731756	type	True	77.5546	57	1770	95	below_threshold
Teredinibacter purpureus	strain=Bs12	GCA_014217335.1	2731756	2731756	type	True	77.2851	55	1770	95	below_threshold
Saccharophagus degradans	strain=2-40	GCA_000013665.1	86304	86304	type	True	77.2772	97	1770	95	below_threshold
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	76.8074	54	1770	95	below_threshold
Agaribacterium haliotis	strain=feces2	GCA_002312815.1	2013869	2013869	type	True	76.7792	58	1770	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:23,867] [INFO] DFAST Taxonomy check result was written to GCF_021655555.1_ASM2165555v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:23,867] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:23,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:23,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ef8e73c-3282-494c-90d0-7faaaa12bc49/dqc_reference/checkm_data
[2024-01-25 19:12:23,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:23,920] [INFO] Task started: CheckM
[2024-01-25 19:12:23,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021655555.1_ASM2165555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021655555.1_ASM2165555v1_genomic.fna/checkm_input GCF_021655555.1_ASM2165555v1_genomic.fna/checkm_result
[2024-01-25 19:13:00,634] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:00,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:00,656] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:00,656] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:00,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021655555.1_ASM2165555v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:00,657] [INFO] Task started: Blastn
[2024-01-25 19:13:00,657] [INFO] Running command: blastn -query GCF_021655555.1_ASM2165555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ef8e73c-3282-494c-90d0-7faaaa12bc49/dqc_reference/reference_markers_gtdb.fasta -out GCF_021655555.1_ASM2165555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:01,681] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:01,684] [INFO] Selected 32 target genomes.
[2024-01-25 19:13:01,684] [INFO] Target genome list was writen to GCF_021655555.1_ASM2165555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:01,730] [INFO] Task started: fastANI
[2024-01-25 19:13:01,730] [INFO] Running command: fastANI --query /var/lib/cwl/stge7cf0188-bea4-4431-84b5-6af43dc79be2/GCF_021655555.1_ASM2165555v1_genomic.fna.gz --refList GCF_021655555.1_ASM2165555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021655555.1_ASM2165555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:23,673] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:23,680] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:13:23,680] [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_014211975.1	s__Teredinibacter haidensis	79.9714	70	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001292705.1	s__Marinagarivorans algicola	78.2572	238	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinagarivorans	95.0	99.28	99.28	0.94	0.94	2	-
GCA_003634075.1	s__Teredinibacter sp003634075	78.257	51	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832015.1	s__Gilvimarinus agarilyticus	77.7691	64	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217335.1	s__Teredinibacter purpureus	77.2836	55	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000013665.1	s__Saccharophagus degradans	77.1436	96	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Saccharophagus	95.0	96.22	96.22	0.89	0.89	2	-
GCF_002312815.1	s__Agaribacterium haliotis	76.7745	57	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Agaribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187555.1	s__Gilvimarinus polysaccharolyticus	76.7595	54	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746115.1	s__GCA-2746115 sp002746115	76.1523	52	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__GCA-2746115	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:23,681] [INFO] GTDB search result was written to GCF_021655555.1_ASM2165555v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:23,681] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:23,684] [INFO] DFAST_QC result json was written to GCF_021655555.1_ASM2165555v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:23,684] [INFO] DFAST_QC completed!
[2024-01-25 19:13:23,684] [INFO] Total running time: 0h1m33s