[2024-01-24 13:55:57,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:57,155] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:57,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg97630d78-f2f3-41ad-be8e-ddd976edd32b/dqc_reference
[2024-01-24 13:55:58,432] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:58,433] [INFO] Task started: Prodigal
[2024-01-24 13:55:58,433] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2b2a954-4f35-4c1d-84ab-b6aaa9ebcffc/GCF_000425405.1_ASM42540v1_genomic.fna.gz | prodigal -d GCF_000425405.1_ASM42540v1_genomic.fna/cds.fna -a GCF_000425405.1_ASM42540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:13,024] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:13,024] [INFO] Task started: HMMsearch
[2024-01-24 13:56:13,025] [INFO] Running command: hmmsearch --tblout GCF_000425405.1_ASM42540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97630d78-f2f3-41ad-be8e-ddd976edd32b/dqc_reference/reference_markers.hmm GCF_000425405.1_ASM42540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:13,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:13,322] [INFO] Found 6/6 markers.
[2024-01-24 13:56:13,367] [INFO] Query marker FASTA was written to GCF_000425405.1_ASM42540v1_genomic.fna/markers.fasta
[2024-01-24 13:56:13,367] [INFO] Task started: Blastn
[2024-01-24 13:56:13,367] [INFO] Running command: blastn -query GCF_000425405.1_ASM42540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97630d78-f2f3-41ad-be8e-ddd976edd32b/dqc_reference/reference_markers.fasta -out GCF_000425405.1_ASM42540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:14,246] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:14,250] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:14,250] [INFO] Target genome list was writen to GCF_000425405.1_ASM42540v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:14,268] [INFO] Task started: fastANI
[2024-01-24 13:56:14,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2b2a954-4f35-4c1d-84ab-b6aaa9ebcffc/GCF_000425405.1_ASM42540v1_genomic.fna.gz --refList GCF_000425405.1_ASM42540v1_genomic.fna/target_genomes.txt --output GCF_000425405.1_ASM42540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:23,577] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:23,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97630d78-f2f3-41ad-be8e-ddd976edd32b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:23,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97630d78-f2f3-41ad-be8e-ddd976edd32b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:23,593] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:23,593] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:23,593] [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 kyonanensis	strain=DSM 18153	GCA_000425405.1	364763	364763	type	True	100.0	1617	1622	95	conclusive
Ferrimonas sediminum	strain=DSM 23317	GCA_900100175.1	718193	718193	type	True	88.8858	1271	1622	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	80.5274	833	1622	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	80.2141	803	1622	95	below_threshold
Ferrimonas aestuarii	strain=IMCC35002	GCA_005116665.1	2569539	2569539	type	True	78.8936	508	1622	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	78.1568	368	1622	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.2229	65	1622	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.1956	67	1622	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	75.8489	71	1622	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	75.7203	81	1622	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	75.546	81	1622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:23,595] [INFO] DFAST Taxonomy check result was written to GCF_000425405.1_ASM42540v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:23,595] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:23,595] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:23,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97630d78-f2f3-41ad-be8e-ddd976edd32b/dqc_reference/checkm_data
[2024-01-24 13:56:23,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:23,643] [INFO] Task started: CheckM
[2024-01-24 13:56:23,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425405.1_ASM42540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425405.1_ASM42540v1_genomic.fna/checkm_input GCF_000425405.1_ASM42540v1_genomic.fna/checkm_result
[2024-01-24 13:57:07,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:07,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:07,959] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:07,960] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:07,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425405.1_ASM42540v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:07,961] [INFO] Task started: Blastn
[2024-01-24 13:57:07,961] [INFO] Running command: blastn -query GCF_000425405.1_ASM42540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97630d78-f2f3-41ad-be8e-ddd976edd32b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425405.1_ASM42540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:09,335] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:09,339] [INFO] Selected 6 target genomes.
[2024-01-24 13:57:09,339] [INFO] Target genome list was writen to GCF_000425405.1_ASM42540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:09,348] [INFO] Task started: fastANI
[2024-01-24 13:57:09,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2b2a954-4f35-4c1d-84ab-b6aaa9ebcffc/GCF_000425405.1_ASM42540v1_genomic.fna.gz --refList GCF_000425405.1_ASM42540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425405.1_ASM42540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:15,969] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:15,978] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:15,978] [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_000425405.1	s__Ferrimonas kyonanensis	100.0	1617	1622	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_900100175.1	s__Ferrimonas sediminum	88.8858	1271	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422645.1	s__Ferrimonas futtsuensis	80.5301	833	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116715.1	s__Ferrimonas sp005116715	80.2212	802	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116665.1	s__Ferrimonas sp005116665	78.8845	509	1622	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	78.1568	368	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:15,980] [INFO] GTDB search result was written to GCF_000425405.1_ASM42540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:15,981] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:15,985] [INFO] DFAST_QC result json was written to GCF_000425405.1_ASM42540v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:15,985] [INFO] DFAST_QC completed!
[2024-01-24 13:57:15,985] [INFO] Total running time: 0h1m19s