[2024-01-24 12:25:20,700] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:25:20,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:25:20,702] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd4c33fa-fcaf-4cf6-8ded-7550bde8c0f8/dqc_reference
[2024-01-24 12:25:21,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:25:21,890] [INFO] Task started: Prodigal
[2024-01-24 12:25:21,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg02447edc-bd66-437d-bed7-cecac72a6104/GCF_014217335.1_ASM1421733v1_genomic.fna.gz | prodigal -d GCF_014217335.1_ASM1421733v1_genomic.fna/cds.fna -a GCF_014217335.1_ASM1421733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:25:33,553] [INFO] Task succeeded: Prodigal
[2024-01-24 12:25:33,554] [INFO] Task started: HMMsearch
[2024-01-24 12:25:33,554] [INFO] Running command: hmmsearch --tblout GCF_014217335.1_ASM1421733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd4c33fa-fcaf-4cf6-8ded-7550bde8c0f8/dqc_reference/reference_markers.hmm GCF_014217335.1_ASM1421733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:25:33,842] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:25:33,843] [INFO] Found 6/6 markers.
[2024-01-24 12:25:33,883] [INFO] Query marker FASTA was written to GCF_014217335.1_ASM1421733v1_genomic.fna/markers.fasta
[2024-01-24 12:25:33,884] [INFO] Task started: Blastn
[2024-01-24 12:25:33,884] [INFO] Running command: blastn -query GCF_014217335.1_ASM1421733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd4c33fa-fcaf-4cf6-8ded-7550bde8c0f8/dqc_reference/reference_markers.fasta -out GCF_014217335.1_ASM1421733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:34,525] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:34,529] [INFO] Selected 20 target genomes.
[2024-01-24 12:25:34,530] [INFO] Target genome list was writen to GCF_014217335.1_ASM1421733v1_genomic.fna/target_genomes.txt
[2024-01-24 12:25:34,538] [INFO] Task started: fastANI
[2024-01-24 12:25:34,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg02447edc-bd66-437d-bed7-cecac72a6104/GCF_014217335.1_ASM1421733v1_genomic.fna.gz --refList GCF_014217335.1_ASM1421733v1_genomic.fna/target_genomes.txt --output GCF_014217335.1_ASM1421733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:25:49,380] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:49,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd4c33fa-fcaf-4cf6-8ded-7550bde8c0f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:25:49,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd4c33fa-fcaf-4cf6-8ded-7550bde8c0f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:25:49,391] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:25:49,392] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:25:49,392] [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 purpureus	strain=Bs12	GCA_014217335.1	2731756	2731756	type	True	100.0	1630	1630	95	conclusive
Teredinibacter purpureus	strain=Bs12	GCA_000966245.1	2731756	2731756	type	True	99.9995	1630	1630	95	conclusive
Teredinibacter haidensis	strain=Bs08	GCA_014211975.1	2731755	2731755	type	True	78.6775	217	1630	95	below_threshold
Agarilytica rhodophyticola	strain=017	GCA_002157225.2	1737490	1737490	type	True	78.1051	50	1630	95	below_threshold
Teredinibacter franksiae	strain=Bsc2	GCA_014218805.1	2761453	2761453	type	True	77.5725	191	1630	95	below_threshold
Teredinibacter waterburyi	strain=Bs02	GCA_001922985.1	1500538	1500538	type	True	77.3633	127	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:25:49,393] [INFO] DFAST Taxonomy check result was written to GCF_014217335.1_ASM1421733v1_genomic.fna/tc_result.tsv
[2024-01-24 12:25:49,394] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:25:49,394] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:25:49,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd4c33fa-fcaf-4cf6-8ded-7550bde8c0f8/dqc_reference/checkm_data
[2024-01-24 12:25:49,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:25:49,446] [INFO] Task started: CheckM
[2024-01-24 12:25:49,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014217335.1_ASM1421733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014217335.1_ASM1421733v1_genomic.fna/checkm_input GCF_014217335.1_ASM1421733v1_genomic.fna/checkm_result
[2024-01-24 12:26:26,801] [INFO] Task succeeded: CheckM
[2024-01-24 12:26:26,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:26:26,827] [INFO] ===== Completeness check finished =====
[2024-01-24 12:26:26,827] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:26:26,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014217335.1_ASM1421733v1_genomic.fna/markers.fasta)
[2024-01-24 12:26:26,828] [INFO] Task started: Blastn
[2024-01-24 12:26:26,828] [INFO] Running command: blastn -query GCF_014217335.1_ASM1421733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd4c33fa-fcaf-4cf6-8ded-7550bde8c0f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014217335.1_ASM1421733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:26:27,678] [INFO] Task succeeded: Blastn
[2024-01-24 12:26:27,683] [INFO] Selected 26 target genomes.
[2024-01-24 12:26:27,683] [INFO] Target genome list was writen to GCF_014217335.1_ASM1421733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:26:27,715] [INFO] Task started: fastANI
[2024-01-24 12:26:27,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg02447edc-bd66-437d-bed7-cecac72a6104/GCF_014217335.1_ASM1421733v1_genomic.fna.gz --refList GCF_014217335.1_ASM1421733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014217335.1_ASM1421733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:44,801] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:44,813] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:44,813] [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_014217335.1	s__Teredinibacter purpureus	100.0	1630	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014211975.1	s__Teredinibacter haidensis	78.7284	214	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002157225.2	s__Agarilytica rhodophyticola	78.0413	50	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Agarilytica	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007827375.1	s__Teredinibacter sp007827375	77.8078	108	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218805.1	s__Teredinibacter franksiae	77.6615	194	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900177435.1	s__Teredinibacter sp900177435	77.5578	139	1630	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	77.3633	127	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000964245.1	s__1162T-S-0a-05 sp000964245	77.1287	58	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__1162T-S-0a-05	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141825.1	s__Thalassocella blandensis	76.7587	66	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Thalassocella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:44,815] [INFO] GTDB search result was written to GCF_014217335.1_ASM1421733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:44,815] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:44,818] [INFO] DFAST_QC result json was written to GCF_014217335.1_ASM1421733v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:44,818] [INFO] DFAST_QC completed!
[2024-01-24 12:26:44,818] [INFO] Total running time: 0h1m24s