[2024-01-25 17:53:50,549] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg52a84e0a-5512-47d2-b897-008b17dc130f/dqc_reference
[2024-01-25 17:53:51,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,747] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,748] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b467c71-8e0c-41f6-895b-a64ad1352c73/GCF_013265555.1_ASM1326555v1_genomic.fna.gz | prodigal -d GCF_013265555.1_ASM1326555v1_genomic.fna/cds.fna -a GCF_013265555.1_ASM1326555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:01,936] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:01,937] [INFO] Task started: HMMsearch
[2024-01-25 17:54:01,937] [INFO] Running command: hmmsearch --tblout GCF_013265555.1_ASM1326555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52a84e0a-5512-47d2-b897-008b17dc130f/dqc_reference/reference_markers.hmm GCF_013265555.1_ASM1326555v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:02,155] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:02,157] [INFO] Found 6/6 markers.
[2024-01-25 17:54:02,185] [INFO] Query marker FASTA was written to GCF_013265555.1_ASM1326555v1_genomic.fna/markers.fasta
[2024-01-25 17:54:02,186] [INFO] Task started: Blastn
[2024-01-25 17:54:02,186] [INFO] Running command: blastn -query GCF_013265555.1_ASM1326555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52a84e0a-5512-47d2-b897-008b17dc130f/dqc_reference/reference_markers.fasta -out GCF_013265555.1_ASM1326555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:02,732] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:02,735] [INFO] Selected 30 target genomes.
[2024-01-25 17:54:02,735] [INFO] Target genome list was writen to GCF_013265555.1_ASM1326555v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:02,784] [INFO] Task started: fastANI
[2024-01-25 17:54:02,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b467c71-8e0c-41f6-895b-a64ad1352c73/GCF_013265555.1_ASM1326555v1_genomic.fna.gz --refList GCF_013265555.1_ASM1326555v1_genomic.fna/target_genomes.txt --output GCF_013265555.1_ASM1326555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:22,323] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:22,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52a84e0a-5512-47d2-b897-008b17dc130f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:22,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52a84e0a-5512-47d2-b897-008b17dc130f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:22,326] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:22,327] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:22,327] [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
Tenuifilum thalassicum	strain=38H-str	GCA_013265555.1	2590900	2590900	type	True	100.0	1065	1065	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:54:22,328] [INFO] DFAST Taxonomy check result was written to GCF_013265555.1_ASM1326555v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:22,329] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:22,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:22,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52a84e0a-5512-47d2-b897-008b17dc130f/dqc_reference/checkm_data
[2024-01-25 17:54:22,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:22,365] [INFO] Task started: CheckM
[2024-01-25 17:54:22,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013265555.1_ASM1326555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013265555.1_ASM1326555v1_genomic.fna/checkm_input GCF_013265555.1_ASM1326555v1_genomic.fna/checkm_result
[2024-01-25 17:54:54,323] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:54,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:54,340] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:54,340] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:54,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013265555.1_ASM1326555v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:54,341] [INFO] Task started: Blastn
[2024-01-25 17:54:54,341] [INFO] Running command: blastn -query GCF_013265555.1_ASM1326555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52a84e0a-5512-47d2-b897-008b17dc130f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013265555.1_ASM1326555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:55,145] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:55,147] [INFO] Selected 21 target genomes.
[2024-01-25 17:54:55,147] [INFO] Target genome list was writen to GCF_013265555.1_ASM1326555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:55,175] [INFO] Task started: fastANI
[2024-01-25 17:54:55,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b467c71-8e0c-41f6-895b-a64ad1352c73/GCF_013265555.1_ASM1326555v1_genomic.fna.gz --refList GCF_013265555.1_ASM1326555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013265555.1_ASM1326555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:55:08,550] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:08,555] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:55:08,556] [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_013265555.1	s__Tenuifilum thalassicum	100.0	1065	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tenuifilaceae;g__Tenuifilum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011367975.1	s__Tenuifilum sp011367975	77.8432	229	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tenuifilaceae;g__Tenuifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011045955.1	s__Tenuifilum sp011045955	77.7166	175	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tenuifilaceae;g__Tenuifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056955.1	s__Tenuifilum sp018056955	77.7081	208	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tenuifilaceae;g__Tenuifilum	95.0	99.52	99.52	0.91	0.91	2	-
GCA_001603415.1	s__Tenuifilum sp001603415	77.5123	159	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tenuifilaceae;g__Tenuifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933525.1	s__SB25 sp008933525	76.6399	76	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tenuifilaceae;g__SB25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141385.1	s__UBA8529 sp013141385	75.8586	57	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tenuifilaceae;g__UBA8529	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:55:08,557] [INFO] GTDB search result was written to GCF_013265555.1_ASM1326555v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:55:08,558] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:55:08,560] [INFO] DFAST_QC result json was written to GCF_013265555.1_ASM1326555v1_genomic.fna/dqc_result.json
[2024-01-25 17:55:08,560] [INFO] DFAST_QC completed!
[2024-01-25 17:55:08,560] [INFO] Total running time: 0h1m18s