[2024-01-25 19:07:05,972] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:05,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:05,974] [INFO] DQC Reference Directory: /var/lib/cwl/stga474602d-e031-4bdf-a3b4-5449e4ba738d/dqc_reference
[2024-01-25 19:07:07,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:07,133] [INFO] Task started: Prodigal
[2024-01-25 19:07:07,134] [INFO] Running command: gunzip -c /var/lib/cwl/stga0565539-2680-4321-b50e-22b7c66e03b3/GCF_000695795.1_ASM69579v1_genomic.fna.gz | prodigal -d GCF_000695795.1_ASM69579v1_genomic.fna/cds.fna -a GCF_000695795.1_ASM69579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:17,328] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:17,328] [INFO] Task started: HMMsearch
[2024-01-25 19:07:17,328] [INFO] Running command: hmmsearch --tblout GCF_000695795.1_ASM69579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga474602d-e031-4bdf-a3b4-5449e4ba738d/dqc_reference/reference_markers.hmm GCF_000695795.1_ASM69579v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:17,540] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:17,541] [INFO] Found 6/6 markers.
[2024-01-25 19:07:17,570] [INFO] Query marker FASTA was written to GCF_000695795.1_ASM69579v1_genomic.fna/markers.fasta
[2024-01-25 19:07:17,571] [INFO] Task started: Blastn
[2024-01-25 19:07:17,571] [INFO] Running command: blastn -query GCF_000695795.1_ASM69579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga474602d-e031-4bdf-a3b4-5449e4ba738d/dqc_reference/reference_markers.fasta -out GCF_000695795.1_ASM69579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:18,216] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:18,221] [INFO] Selected 17 target genomes.
[2024-01-25 19:07:18,221] [INFO] Target genome list was writen to GCF_000695795.1_ASM69579v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:18,239] [INFO] Task started: fastANI
[2024-01-25 19:07:18,239] [INFO] Running command: fastANI --query /var/lib/cwl/stga0565539-2680-4321-b50e-22b7c66e03b3/GCF_000695795.1_ASM69579v1_genomic.fna.gz --refList GCF_000695795.1_ASM69579v1_genomic.fna/target_genomes.txt --output GCF_000695795.1_ASM69579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:32,920] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:32,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga474602d-e031-4bdf-a3b4-5449e4ba738d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:32,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga474602d-e031-4bdf-a3b4-5449e4ba738d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:32,932] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:07:32,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:32,932] [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
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	100.0	1229	1235	95	conclusive
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	84.3985	871	1235	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	84.0039	849	1235	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	83.9011	816	1235	95	below_threshold
Flavobacterium palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	83.4074	879	1235	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	83.3949	826	1235	95	below_threshold
Flavobacterium flevense	strain=DSM 1076	GCA_900142775.1	983	983	type	True	83.3073	863	1235	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_001686935.1	551990	551990	type	True	82.9433	803	1235	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_007989005.1	551990	551990	type	True	82.9107	806	1235	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	82.8985	794	1235	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	81.827	762	1235	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	79.0758	445	1235	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.9029	505	1235	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	78.8813	500	1235	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.8749	461	1235	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.8587	460	1235	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.0704	155	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:32,934] [INFO] DFAST Taxonomy check result was written to GCF_000695795.1_ASM69579v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:32,934] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:32,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:32,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga474602d-e031-4bdf-a3b4-5449e4ba738d/dqc_reference/checkm_data
[2024-01-25 19:07:32,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:32,973] [INFO] Task started: CheckM
[2024-01-25 19:07:32,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000695795.1_ASM69579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000695795.1_ASM69579v1_genomic.fna/checkm_input GCF_000695795.1_ASM69579v1_genomic.fna/checkm_result
[2024-01-25 19:08:06,526] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:06,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:06,544] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:06,545] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:06,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000695795.1_ASM69579v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:06,546] [INFO] Task started: Blastn
[2024-01-25 19:08:06,546] [INFO] Running command: blastn -query GCF_000695795.1_ASM69579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga474602d-e031-4bdf-a3b4-5449e4ba738d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000695795.1_ASM69579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:07,535] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:07,538] [INFO] Selected 10 target genomes.
[2024-01-25 19:08:07,539] [INFO] Target genome list was writen to GCF_000695795.1_ASM69579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:07,558] [INFO] Task started: fastANI
[2024-01-25 19:08:07,559] [INFO] Running command: fastANI --query /var/lib/cwl/stga0565539-2680-4321-b50e-22b7c66e03b3/GCF_000695795.1_ASM69579v1_genomic.fna.gz --refList GCF_000695795.1_ASM69579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000695795.1_ASM69579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:16,697] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:16,704] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:16,704] [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_000695795.1	s__Flavobacterium seoulense	100.0	1229	1235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002280815.1	s__Flavobacterium sp002280815	84.4124	657	1235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001857965.1	s__Flavobacterium commune	84.3784	872	1235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.64	0.89	0.89	2	-
GCF_004016525.1	s__Flavobacterium sufflavum	84.0275	846	1235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	83.8805	820	1235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639535.1	s__Flavobacterium palustre	83.4208	875	1235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142775.1	s__Flavobacterium flevense	83.2795	866	1235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100165.1	s__Flavobacterium glycines	82.8882	794	1235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000425425.1	s__Flavobacterium daejeonense	81.8269	762	1235	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	81.6096	447	1235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:08:16,706] [INFO] GTDB search result was written to GCF_000695795.1_ASM69579v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:16,706] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:16,709] [INFO] DFAST_QC result json was written to GCF_000695795.1_ASM69579v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:16,709] [INFO] DFAST_QC completed!
[2024-01-25 19:08:16,709] [INFO] Total running time: 0h1m11s