[2024-01-24 13:49:25,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:25,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:25,353] [INFO] DQC Reference Directory: /var/lib/cwl/stge5a6802c-d670-4ac1-b1cb-879981c61ef2/dqc_reference
[2024-01-24 13:49:26,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:26,671] [INFO] Task started: Prodigal
[2024-01-24 13:49:26,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg93690a6e-03a1-4ab0-a59c-f242eda10dab/GCF_014211975.1_ASM1421197v1_genomic.fna.gz | prodigal -d GCF_014211975.1_ASM1421197v1_genomic.fna/cds.fna -a GCF_014211975.1_ASM1421197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,847] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,847] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,847] [INFO] Running command: hmmsearch --tblout GCF_014211975.1_ASM1421197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5a6802c-d670-4ac1-b1cb-879981c61ef2/dqc_reference/reference_markers.hmm GCF_014211975.1_ASM1421197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:43,118] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:43,119] [INFO] Found 6/6 markers.
[2024-01-24 13:49:43,163] [INFO] Query marker FASTA was written to GCF_014211975.1_ASM1421197v1_genomic.fna/markers.fasta
[2024-01-24 13:49:43,164] [INFO] Task started: Blastn
[2024-01-24 13:49:43,164] [INFO] Running command: blastn -query GCF_014211975.1_ASM1421197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5a6802c-d670-4ac1-b1cb-879981c61ef2/dqc_reference/reference_markers.fasta -out GCF_014211975.1_ASM1421197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,891] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,899] [INFO] Selected 31 target genomes.
[2024-01-24 13:49:43,900] [INFO] Target genome list was writen to GCF_014211975.1_ASM1421197v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,922] [INFO] Task started: fastANI
[2024-01-24 13:49:43,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg93690a6e-03a1-4ab0-a59c-f242eda10dab/GCF_014211975.1_ASM1421197v1_genomic.fna.gz --refList GCF_014211975.1_ASM1421197v1_genomic.fna/target_genomes.txt --output GCF_014211975.1_ASM1421197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:04,958] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5a6802c-d670-4ac1-b1cb-879981c61ef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:04,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5a6802c-d670-4ac1-b1cb-879981c61ef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:04,968] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:04,969] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:04,969] [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	100.0	1637	1638	95	conclusive
Teredinibacter purpureus	strain=Bs12	GCA_000966245.1	2731756	2731756	type	True	78.4285	229	1638	95	below_threshold
Teredinibacter purpureus	strain=Bs12	GCA_014217335.1	2731756	2731756	type	True	78.3499	231	1638	95	below_threshold
Teredinibacter franksiae	strain=Bsc2	GCA_014218805.1	2761453	2761453	type	True	77.9061	232	1638	95	below_threshold
Teredinibacter turnerae	strain=T7902	GCA_000379165.1	2426	2426	type	True	77.7811	147	1638	95	below_threshold
Microbulbifer hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	77.4228	50	1638	95	below_threshold
Saccharophagus degradans	strain=2-40	GCA_000013665.1	86304	86304	type	True	77.4127	115	1638	95	below_threshold
Teredinibacter waterburyi	strain=Bs02	GCA_001922985.1	1500538	1500538	type	True	77.1593	117	1638	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	76.8752	57	1638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,970] [INFO] DFAST Taxonomy check result was written to GCF_014211975.1_ASM1421197v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:04,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:04,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:04,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5a6802c-d670-4ac1-b1cb-879981c61ef2/dqc_reference/checkm_data
[2024-01-24 13:50:04,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:05,020] [INFO] Task started: CheckM
[2024-01-24 13:50:05,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014211975.1_ASM1421197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014211975.1_ASM1421197v1_genomic.fna/checkm_input GCF_014211975.1_ASM1421197v1_genomic.fna/checkm_result
[2024-01-24 13:50:55,003] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:55,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:55,020] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:55,021] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:55,021] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014211975.1_ASM1421197v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:55,021] [INFO] Task started: Blastn
[2024-01-24 13:50:55,021] [INFO] Running command: blastn -query GCF_014211975.1_ASM1421197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5a6802c-d670-4ac1-b1cb-879981c61ef2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014211975.1_ASM1421197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:56,081] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:56,084] [INFO] Selected 27 target genomes.
[2024-01-24 13:50:56,084] [INFO] Target genome list was writen to GCF_014211975.1_ASM1421197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:56,111] [INFO] Task started: fastANI
[2024-01-24 13:50:56,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg93690a6e-03a1-4ab0-a59c-f242eda10dab/GCF_014211975.1_ASM1421197v1_genomic.fna.gz --refList GCF_014211975.1_ASM1421197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014211975.1_ASM1421197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:15,096] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:15,105] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:15,105] [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	100.0	1637	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_014217335.1	s__Teredinibacter purpureus	78.4035	228	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014218805.1	s__Teredinibacter franksiae	77.9005	234	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379165.1	s__Teredinibacter turnerae	77.811	145	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	98.03	97.55	0.91	0.90	6	-
GCF_000023025.1	s__Teredinibacter turnerae_B	77.732	147	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	98.16	98.08	0.93	0.93	4	-
GCA_003634075.1	s__Teredinibacter sp003634075	77.4715	188	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013665.1	s__Saccharophagus degradans	77.2839	115	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Saccharophagus	95.0	96.22	96.22	0.89	0.89	2	-
GCA_900177435.1	s__Teredinibacter sp900177435	77.2059	178	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001922985.1	s__Teredinibacter waterburyi	77.2055	115	1638	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 13:51:15,107] [INFO] GTDB search result was written to GCF_014211975.1_ASM1421197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:15,107] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:15,111] [INFO] DFAST_QC result json was written to GCF_014211975.1_ASM1421197v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:15,111] [INFO] DFAST_QC completed!
[2024-01-24 13:51:15,111] [INFO] Total running time: 0h1m50s