[2024-01-24 12:31:51,189] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgda26d8df-49a2-4d7c-b30e-caf848f26ce4/dqc_reference
[2024-01-24 12:31:52,504] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,505] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg75cfea31-4da3-4a6d-8160-5138c0047355/GCF_024347255.1_ASM2434725v1_genomic.fna.gz | prodigal -d GCF_024347255.1_ASM2434725v1_genomic.fna/cds.fna -a GCF_024347255.1_ASM2434725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:08,593] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:08,594] [INFO] Task started: HMMsearch
[2024-01-24 12:32:08,594] [INFO] Running command: hmmsearch --tblout GCF_024347255.1_ASM2434725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda26d8df-49a2-4d7c-b30e-caf848f26ce4/dqc_reference/reference_markers.hmm GCF_024347255.1_ASM2434725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:08,873] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:08,874] [INFO] Found 6/6 markers.
[2024-01-24 12:32:08,918] [INFO] Query marker FASTA was written to GCF_024347255.1_ASM2434725v1_genomic.fna/markers.fasta
[2024-01-24 12:32:08,919] [INFO] Task started: Blastn
[2024-01-24 12:32:08,919] [INFO] Running command: blastn -query GCF_024347255.1_ASM2434725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda26d8df-49a2-4d7c-b30e-caf848f26ce4/dqc_reference/reference_markers.fasta -out GCF_024347255.1_ASM2434725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:09,551] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:09,555] [INFO] Selected 18 target genomes.
[2024-01-24 12:32:09,556] [INFO] Target genome list was writen to GCF_024347255.1_ASM2434725v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:09,572] [INFO] Task started: fastANI
[2024-01-24 12:32:09,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg75cfea31-4da3-4a6d-8160-5138c0047355/GCF_024347255.1_ASM2434725v1_genomic.fna.gz --refList GCF_024347255.1_ASM2434725v1_genomic.fna/target_genomes.txt --output GCF_024347255.1_ASM2434725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:23,399] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:23,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda26d8df-49a2-4d7c-b30e-caf848f26ce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:23,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda26d8df-49a2-4d7c-b30e-caf848f26ce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:23,415] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:23,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:23,415] [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
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	99.9863	1554	1601	95	conclusive
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	94.1298	1325	1601	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	79.6885	582	1601	95	below_threshold
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	79.5304	560	1601	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	79.4965	561	1601	95	below_threshold
Amphritea japonica	strain=JAMM 1866	GCA_000381785.1	452627	452627	type	True	79.3104	547	1601	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	79.2135	406	1601	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	79.1269	402	1601	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	78.8044	191	1601	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	78.5087	224	1601	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	77.0823	143	1601	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	77.0592	135	1601	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.906	173	1601	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	76.7086	98	1601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:23,417] [INFO] DFAST Taxonomy check result was written to GCF_024347255.1_ASM2434725v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:23,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:23,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:23,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda26d8df-49a2-4d7c-b30e-caf848f26ce4/dqc_reference/checkm_data
[2024-01-24 12:32:23,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:23,467] [INFO] Task started: CheckM
[2024-01-24 12:32:23,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347255.1_ASM2434725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347255.1_ASM2434725v1_genomic.fna/checkm_input GCF_024347255.1_ASM2434725v1_genomic.fna/checkm_result
[2024-01-24 12:33:13,919] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:13,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:13,956] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:13,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:13,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347255.1_ASM2434725v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:13,957] [INFO] Task started: Blastn
[2024-01-24 12:33:13,957] [INFO] Running command: blastn -query GCF_024347255.1_ASM2434725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda26d8df-49a2-4d7c-b30e-caf848f26ce4/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347255.1_ASM2434725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:14,809] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:14,814] [INFO] Selected 9 target genomes.
[2024-01-24 12:33:14,814] [INFO] Target genome list was writen to GCF_024347255.1_ASM2434725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:14,847] [INFO] Task started: fastANI
[2024-01-24 12:33:14,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg75cfea31-4da3-4a6d-8160-5138c0047355/GCF_024347255.1_ASM2434725v1_genomic.fna.gz --refList GCF_024347255.1_ASM2434725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347255.1_ASM2434725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:24,524] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:24,542] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:24,542] [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_900111095.1	s__Amphritea atlantica	99.9863	1554	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016924235.1	s__Amphritea sp016924235	94.1257	1340	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCA_018223185.1	s__Amphritea sp018223185	83.2632	1057	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCF_003957515.1	s__Amphritea opalescens	79.7104	579	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860855.1	s__Amphritea atlantica_A	79.6678	581	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858655.1	s__Amphritea balenae	79.2136	406	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016744155.1	s__Amphritea sp016744155	78.8807	592	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051665.1	s__Amphritea spongicola	78.5233	222	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	77.078	143	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:24,545] [INFO] GTDB search result was written to GCF_024347255.1_ASM2434725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:24,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:24,551] [INFO] DFAST_QC result json was written to GCF_024347255.1_ASM2434725v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:24,551] [INFO] DFAST_QC completed!
[2024-01-24 12:33:24,551] [INFO] Total running time: 0h1m33s