[2024-01-24 12:27:19,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:19,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:19,272] [INFO] DQC Reference Directory: /var/lib/cwl/stgc131eeab-c246-4f8e-a038-be5fbf6a3d5b/dqc_reference
[2024-01-24 12:27:20,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:20,469] [INFO] Task started: Prodigal
[2024-01-24 12:27:20,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg147b319e-880e-4486-9487-1b562e9bc0d9/GCF_005116715.1_ASM511671v1_genomic.fna.gz | prodigal -d GCF_005116715.1_ASM511671v1_genomic.fna/cds.fna -a GCF_005116715.1_ASM511671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:31,893] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:31,893] [INFO] Task started: HMMsearch
[2024-01-24 12:27:31,893] [INFO] Running command: hmmsearch --tblout GCF_005116715.1_ASM511671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc131eeab-c246-4f8e-a038-be5fbf6a3d5b/dqc_reference/reference_markers.hmm GCF_005116715.1_ASM511671v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:32,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:32,141] [INFO] Found 6/6 markers.
[2024-01-24 12:27:32,178] [INFO] Query marker FASTA was written to GCF_005116715.1_ASM511671v1_genomic.fna/markers.fasta
[2024-01-24 12:27:32,179] [INFO] Task started: Blastn
[2024-01-24 12:27:32,179] [INFO] Running command: blastn -query GCF_005116715.1_ASM511671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc131eeab-c246-4f8e-a038-be5fbf6a3d5b/dqc_reference/reference_markers.fasta -out GCF_005116715.1_ASM511671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:33,096] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:33,100] [INFO] Selected 11 target genomes.
[2024-01-24 12:27:33,100] [INFO] Target genome list was writen to GCF_005116715.1_ASM511671v1_genomic.fna/target_genomes.txt
[2024-01-24 12:27:33,125] [INFO] Task started: fastANI
[2024-01-24 12:27:33,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg147b319e-880e-4486-9487-1b562e9bc0d9/GCF_005116715.1_ASM511671v1_genomic.fna.gz --refList GCF_005116715.1_ASM511671v1_genomic.fna/target_genomes.txt --output GCF_005116715.1_ASM511671v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:27:43,947] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:43,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc131eeab-c246-4f8e-a038-be5fbf6a3d5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:27:43,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc131eeab-c246-4f8e-a038-be5fbf6a3d5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:27:43,962] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:27:43,963] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:27:43,963] [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
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	100.0	1302	1302	95	conclusive
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	85.7382	1088	1302	95	below_threshold
Ferrimonas sediminum	strain=DSM 23317	GCA_900100175.1	718193	718193	type	True	80.5285	853	1302	95	below_threshold
Ferrimonas kyonanensis	strain=DSM 18153	GCA_000425405.1	364763	364763	type	True	80.2672	815	1302	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	79.0547	512	1302	95	below_threshold
Ferrimonas aestuarii	strain=IMCC35002	GCA_005116665.1	2569539	2569539	type	True	78.4185	397	1302	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	76.6143	145	1302	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.5454	170	1302	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	76.4151	143	1302	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.3315	170	1302	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.1852	131	1302	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:27:43,964] [INFO] DFAST Taxonomy check result was written to GCF_005116715.1_ASM511671v1_genomic.fna/tc_result.tsv
[2024-01-24 12:27:43,965] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:27:43,965] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:27:43,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc131eeab-c246-4f8e-a038-be5fbf6a3d5b/dqc_reference/checkm_data
[2024-01-24 12:27:43,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:27:44,009] [INFO] Task started: CheckM
[2024-01-24 12:27:44,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116715.1_ASM511671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116715.1_ASM511671v1_genomic.fna/checkm_input GCF_005116715.1_ASM511671v1_genomic.fna/checkm_result
[2024-01-24 12:28:20,204] [INFO] Task succeeded: CheckM
[2024-01-24 12:28:20,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:28:20,234] [INFO] ===== Completeness check finished =====
[2024-01-24 12:28:20,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:28:20,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116715.1_ASM511671v1_genomic.fna/markers.fasta)
[2024-01-24 12:28:20,235] [INFO] Task started: Blastn
[2024-01-24 12:28:20,235] [INFO] Running command: blastn -query GCF_005116715.1_ASM511671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc131eeab-c246-4f8e-a038-be5fbf6a3d5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116715.1_ASM511671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:21,775] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:21,779] [INFO] Selected 6 target genomes.
[2024-01-24 12:28:21,779] [INFO] Target genome list was writen to GCF_005116715.1_ASM511671v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:28:21,824] [INFO] Task started: fastANI
[2024-01-24 12:28:21,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg147b319e-880e-4486-9487-1b562e9bc0d9/GCF_005116715.1_ASM511671v1_genomic.fna.gz --refList GCF_005116715.1_ASM511671v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005116715.1_ASM511671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:28:27,586] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:27,598] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:28:27,598] [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_005116715.1	s__Ferrimonas sp005116715	100.0	1302	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000422645.1	s__Ferrimonas futtsuensis	85.7402	1088	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100175.1	s__Ferrimonas sediminum	80.5216	854	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425405.1	s__Ferrimonas kyonanensis	80.2787	813	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129905.1	s__Ferrimonas marina	79.0431	513	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005116665.1	s__Ferrimonas sp005116665	78.4193	397	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:28:27,601] [INFO] GTDB search result was written to GCF_005116715.1_ASM511671v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:28:27,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:28:27,606] [INFO] DFAST_QC result json was written to GCF_005116715.1_ASM511671v1_genomic.fna/dqc_result.json
[2024-01-24 12:28:27,606] [INFO] DFAST_QC completed!
[2024-01-24 12:28:27,607] [INFO] Total running time: 0h1m8s