[2024-01-24 14:03:01,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:01,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:01,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg151b1b37-42eb-485b-9486-05038b4fc90d/dqc_reference
[2024-01-24 14:03:03,187] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:03,188] [INFO] Task started: Prodigal
[2024-01-24 14:03:03,188] [INFO] Running command: gunzip -c /var/lib/cwl/stg702e9a8e-6b87-4333-8c0d-dc3e19cee3d9/GCF_014218805.1_ASM1421880v1_genomic.fna.gz | prodigal -d GCF_014218805.1_ASM1421880v1_genomic.fna/cds.fna -a GCF_014218805.1_ASM1421880v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:16,669] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:16,670] [INFO] Task started: HMMsearch
[2024-01-24 14:03:16,670] [INFO] Running command: hmmsearch --tblout GCF_014218805.1_ASM1421880v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg151b1b37-42eb-485b-9486-05038b4fc90d/dqc_reference/reference_markers.hmm GCF_014218805.1_ASM1421880v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:17,066] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:17,068] [INFO] Found 6/6 markers.
[2024-01-24 14:03:17,119] [INFO] Query marker FASTA was written to GCF_014218805.1_ASM1421880v1_genomic.fna/markers.fasta
[2024-01-24 14:03:17,119] [INFO] Task started: Blastn
[2024-01-24 14:03:17,119] [INFO] Running command: blastn -query GCF_014218805.1_ASM1421880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg151b1b37-42eb-485b-9486-05038b4fc90d/dqc_reference/reference_markers.fasta -out GCF_014218805.1_ASM1421880v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:17,881] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:17,885] [INFO] Selected 26 target genomes.
[2024-01-24 14:03:17,885] [INFO] Target genome list was writen to GCF_014218805.1_ASM1421880v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:17,904] [INFO] Task started: fastANI
[2024-01-24 14:03:17,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg702e9a8e-6b87-4333-8c0d-dc3e19cee3d9/GCF_014218805.1_ASM1421880v1_genomic.fna.gz --refList GCF_014218805.1_ASM1421880v1_genomic.fna/target_genomes.txt --output GCF_014218805.1_ASM1421880v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:35,832] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:35,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg151b1b37-42eb-485b-9486-05038b4fc90d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:35,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg151b1b37-42eb-485b-9486-05038b4fc90d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:35,841] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:35,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:35,841] [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 franksiae	strain=Bsc2	GCA_014218805.1	2761453	2761453	type	True	100.0	1796	1798	95	conclusive
Teredinibacter haidensis	strain=Bs08	GCA_014211975.1	2731755	2731755	type	True	77.9894	238	1798	95	below_threshold
Teredinibacter purpureus	strain=Bs12	GCA_014217335.1	2731756	2731756	type	True	77.7208	182	1798	95	below_threshold
Teredinibacter purpureus	strain=Bs12	GCA_000966245.1	2731756	2731756	type	True	77.6954	185	1798	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	77.3413	51	1798	95	below_threshold
Teredinibacter turnerae	strain=T7902	GCA_000379165.1	2426	2426	type	True	76.8543	126	1798	95	below_threshold
Agaribacterium haliotis	strain=feces2	GCA_002312815.1	2013869	2013869	type	True	76.6051	59	1798	95	below_threshold
Teredinibacter waterburyi	strain=Bs02	GCA_001922985.1	1500538	1500538	type	True	76.5976	101	1798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:35,843] [INFO] DFAST Taxonomy check result was written to GCF_014218805.1_ASM1421880v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:35,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:35,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:35,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg151b1b37-42eb-485b-9486-05038b4fc90d/dqc_reference/checkm_data
[2024-01-24 14:03:35,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:35,897] [INFO] Task started: CheckM
[2024-01-24 14:03:35,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014218805.1_ASM1421880v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014218805.1_ASM1421880v1_genomic.fna/checkm_input GCF_014218805.1_ASM1421880v1_genomic.fna/checkm_result
[2024-01-24 14:04:19,556] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:19,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:19,579] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:19,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:19,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014218805.1_ASM1421880v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:19,580] [INFO] Task started: Blastn
[2024-01-24 14:04:19,580] [INFO] Running command: blastn -query GCF_014218805.1_ASM1421880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg151b1b37-42eb-485b-9486-05038b4fc90d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014218805.1_ASM1421880v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:20,669] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:20,674] [INFO] Selected 23 target genomes.
[2024-01-24 14:04:20,674] [INFO] Target genome list was writen to GCF_014218805.1_ASM1421880v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:20,713] [INFO] Task started: fastANI
[2024-01-24 14:04:20,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg702e9a8e-6b87-4333-8c0d-dc3e19cee3d9/GCF_014218805.1_ASM1421880v1_genomic.fna.gz --refList GCF_014218805.1_ASM1421880v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014218805.1_ASM1421880v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:36,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:37,012] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:37,012] [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_014218805.1	s__Teredinibacter franksiae	100.0	1797	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900177435.1	s__Teredinibacter sp900177435	78.3004	216	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014211975.1	s__Teredinibacter haidensis	77.8911	239	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014217335.1	s__Teredinibacter purpureus	77.6968	181	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000023025.1	s__Teredinibacter turnerae_B	77.6299	125	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	98.16	98.08	0.93	0.93	4	-
GCF_015182315.1	s__Cellvibrio polysaccharolyticus	77.5751	52	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007827375.1	s__Teredinibacter sp007827375	77.3789	140	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003634075.1	s__Teredinibacter sp003634075	77.1916	168	1798	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	77.1749	53	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379165.1	s__Teredinibacter turnerae	76.8543	126	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	98.03	97.55	0.91	0.90	6	-
GCF_001922985.1	s__Teredinibacter waterburyi	76.5976	101	1798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:37,014] [INFO] GTDB search result was written to GCF_014218805.1_ASM1421880v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:37,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:37,018] [INFO] DFAST_QC result json was written to GCF_014218805.1_ASM1421880v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:37,018] [INFO] DFAST_QC completed!
[2024-01-24 14:04:37,018] [INFO] Total running time: 0h1m35s