[2024-01-24 13:49:25,567] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:25,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:25,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg74960df6-baef-4bed-824e-5eeb6e8c35eb/dqc_reference
[2024-01-24 13:49:26,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:26,997] [INFO] Task started: Prodigal
[2024-01-24 13:49:26,997] [INFO] Running command: gunzip -c /var/lib/cwl/stg354f9528-750a-40e6-ad7a-db56b8a81f12/GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/cds.fna -a GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:38,888] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:38,889] [INFO] Task started: HMMsearch
[2024-01-24 13:49:38,889] [INFO] Running command: hmmsearch --tblout GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74960df6-baef-4bed-824e-5eeb6e8c35eb/dqc_reference/reference_markers.hmm GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:39,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:39,229] [INFO] Found 6/6 markers.
[2024-01-24 13:49:39,264] [INFO] Query marker FASTA was written to GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:39,264] [INFO] Task started: Blastn
[2024-01-24 13:49:39,265] [INFO] Running command: blastn -query GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg74960df6-baef-4bed-824e-5eeb6e8c35eb/dqc_reference/reference_markers.fasta -out GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:40,007] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:40,011] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:40,012] [INFO] Target genome list was writen to GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:40,021] [INFO] Task started: fastANI
[2024-01-24 13:49:40,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg354f9528-750a-40e6-ad7a-db56b8a81f12/GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna.gz --refList GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:47,707] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:47,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74960df6-baef-4bed-824e-5eeb6e8c35eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:47,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74960df6-baef-4bed-824e-5eeb6e8c35eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:47,715] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:47,715] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:49:47,716] [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
Myroides profundi	strain=DSM 19823	GCA_900111065.1	480520	480520	type	True	100.0	1313	1318	95	inconclusive
Myroides profundi	strain=D25	GCA_000833025.1	480520	480520	type	True	99.9918	1316	1318	95	inconclusive
Myroides odoratimimus subsp. xuanwuensis	strain=DSM 27251	GCA_900142635.1	1324934	76832	type	True	95.0831	1183	1318	95	inconclusive
Myroides odoratimimus	strain=CCUG39352	GCA_001485415.1	76832	76832	type	True	94.9165	1139	1318	95	below_threshold
Myroides odoratimimus	strain=NCTC11180	GCA_900453765.1	76832	76832	type	True	94.8782	1165	1318	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	83.5052	889	1318	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	76.83	102	1318	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:47,717] [INFO] DFAST Taxonomy check result was written to GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:49:47,718] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:47,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:47,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74960df6-baef-4bed-824e-5eeb6e8c35eb/dqc_reference/checkm_data
[2024-01-24 13:49:47,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:47,761] [INFO] Task started: CheckM
[2024-01-24 13:49:47,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/checkm_input GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:25,468] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:25,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:25,496] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:25,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:25,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:25,498] [INFO] Task started: Blastn
[2024-01-24 13:50:25,498] [INFO] Running command: blastn -query GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg74960df6-baef-4bed-824e-5eeb6e8c35eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:26,436] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:26,440] [INFO] Selected 7 target genomes.
[2024-01-24 13:50:26,441] [INFO] Target genome list was writen to GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:26,453] [INFO] Task started: fastANI
[2024-01-24 13:50:26,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg354f9528-750a-40e6-ad7a-db56b8a81f12/GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna.gz --refList GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:32,544] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:32,556] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:32,556] [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_000833025.1	s__Flavobacterium profundi	99.9918	1316	1318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001485415.1	s__Flavobacterium odoratimimum	94.8906	1140	1318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.35	97.00	0.91	0.88	14	-
GCF_900109075.1	s__Flavobacterium marinum_A	83.5401	885	1318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.56	0.90	0.90	4	-
GCF_002286775.1	s__Flavobacterium sp002286775	82.5041	877	1318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711045.1	s__Flavobacterium album_A	81.3622	477	1318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.30	99.30	0.90	0.90	2	-
GCF_009799805.1	s__Flavobacterium phaeum_A	80.0091	464	1318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454195.1	s__Flavobacterium sp002454195	76.9664	61	1318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:32,558] [INFO] GTDB search result was written to GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:32,558] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:32,562] [INFO] DFAST_QC result json was written to GCF_900111065.1_IMG-taxon_2622736514_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:50:32,562] [INFO] DFAST_QC completed!
[2024-01-24 13:50:32,562] [INFO] Total running time: 0h1m7s