[2024-01-25 19:59:50,798] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:50,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:50,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg8be54842-9e63-43fb-b49f-b1ed74aa5e81/dqc_reference
[2024-01-25 19:59:51,944] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:51,944] [INFO] Task started: Prodigal
[2024-01-25 19:59:51,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c6eac46-154d-4c3b-8389-f1d420aaf87a/GCF_000769935.1_ASM76993v1_genomic.fna.gz | prodigal -d GCF_000769935.1_ASM76993v1_genomic.fna/cds.fna -a GCF_000769935.1_ASM76993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:07,447] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:07,447] [INFO] Task started: HMMsearch
[2024-01-25 20:00:07,447] [INFO] Running command: hmmsearch --tblout GCF_000769935.1_ASM76993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8be54842-9e63-43fb-b49f-b1ed74aa5e81/dqc_reference/reference_markers.hmm GCF_000769935.1_ASM76993v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:07,676] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:07,677] [INFO] Found 6/6 markers.
[2024-01-25 20:00:07,714] [INFO] Query marker FASTA was written to GCF_000769935.1_ASM76993v1_genomic.fna/markers.fasta
[2024-01-25 20:00:07,714] [INFO] Task started: Blastn
[2024-01-25 20:00:07,714] [INFO] Running command: blastn -query GCF_000769935.1_ASM76993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8be54842-9e63-43fb-b49f-b1ed74aa5e81/dqc_reference/reference_markers.fasta -out GCF_000769935.1_ASM76993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:08,327] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:08,330] [INFO] Selected 12 target genomes.
[2024-01-25 20:00:08,330] [INFO] Target genome list was writen to GCF_000769935.1_ASM76993v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:08,336] [INFO] Task started: fastANI
[2024-01-25 20:00:08,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c6eac46-154d-4c3b-8389-f1d420aaf87a/GCF_000769935.1_ASM76993v1_genomic.fna.gz --refList GCF_000769935.1_ASM76993v1_genomic.fna/target_genomes.txt --output GCF_000769935.1_ASM76993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:18,219] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:18,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8be54842-9e63-43fb-b49f-b1ed74aa5e81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:18,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8be54842-9e63-43fb-b49f-b1ed74aa5e81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:18,227] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:00:18,227] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:18,227] [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 subsaxonicum	strain=WB 4.1-42	GCA_000769935.1	426226	426226	type	True	100.0	1514	1518	95	conclusive
Flavobacterium subsaxonicum	strain=DSM 21790	GCA_000422725.1	426226	426226	type	True	99.9956	1515	1518	95	conclusive
Flavobacterium zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	83.3995	957	1518	95	below_threshold
Flavobacterium rivuli	strain=WB 3.3-2	GCA_000769825.1	498301	498301	type	True	80.2435	699	1518	95	below_threshold
Flavobacterium rivuli	strain=DSM 21788	GCA_000378485.1	498301	498301	type	True	80.2205	709	1518	95	below_threshold
Flavobacterium akiainvivens	strain=IK-1	GCA_001278115.1	1202724	1202724	type	True	78.5046	547	1518	95	below_threshold
Flavobacterium akiainvivens	strain=DSM 25510	GCA_900115875.1	1202724	1202724	type	True	78.5013	544	1518	95	below_threshold
Flavobacterium beibuense	strain=F44-8	GCA_000769915.1	657326	657326	type	True	77.9133	291	1518	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.7224	319	1518	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	77.542	235	1518	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.0884	91	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:18,229] [INFO] DFAST Taxonomy check result was written to GCF_000769935.1_ASM76993v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:18,229] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:18,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:18,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8be54842-9e63-43fb-b49f-b1ed74aa5e81/dqc_reference/checkm_data
[2024-01-25 20:00:18,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:18,274] [INFO] Task started: CheckM
[2024-01-25 20:00:18,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000769935.1_ASM76993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000769935.1_ASM76993v1_genomic.fna/checkm_input GCF_000769935.1_ASM76993v1_genomic.fna/checkm_result
[2024-01-25 20:01:01,121] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:01,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:01,139] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:01,139] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:01,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000769935.1_ASM76993v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:01,139] [INFO] Task started: Blastn
[2024-01-25 20:01:01,139] [INFO] Running command: blastn -query GCF_000769935.1_ASM76993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8be54842-9e63-43fb-b49f-b1ed74aa5e81/dqc_reference/reference_markers_gtdb.fasta -out GCF_000769935.1_ASM76993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:01,968] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:01,971] [INFO] Selected 8 target genomes.
[2024-01-25 20:01:01,971] [INFO] Target genome list was writen to GCF_000769935.1_ASM76993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:01,979] [INFO] Task started: fastANI
[2024-01-25 20:01:01,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c6eac46-154d-4c3b-8389-f1d420aaf87a/GCF_000769935.1_ASM76993v1_genomic.fna.gz --refList GCF_000769935.1_ASM76993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000769935.1_ASM76993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:09,627] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:09,633] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:09,633] [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_000422725.1	s__Flavobacterium subsaxonicum	99.9956	1515	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_007097145.1	s__Flavobacterium sp007097145	83.4072	956	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378485.1	s__Flavobacterium rivuli	80.2185	710	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009826935.1	s__Flavobacterium sp009826935	78.9213	529	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403075.1	s__Flavobacterium sp003403075	78.7757	538	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278115.1	s__Flavobacterium akiainvivens	78.4986	548	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001708385.1	s__Flavobacterium psychrophilum_A	78.3803	431	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004028155.1	s__Flavobacterium cerinum	78.3064	342	1518	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 20:01:09,635] [INFO] GTDB search result was written to GCF_000769935.1_ASM76993v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:09,635] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:09,638] [INFO] DFAST_QC result json was written to GCF_000769935.1_ASM76993v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:09,638] [INFO] DFAST_QC completed!
[2024-01-25 20:01:09,638] [INFO] Total running time: 0h1m19s