[2024-01-25 19:41:35,520] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:35,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:35,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg5be61480-62a6-47e4-9811-689fa95841b0/dqc_reference
[2024-01-25 19:41:36,732] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:36,732] [INFO] Task started: Prodigal
[2024-01-25 19:41:36,733] [INFO] Running command: gunzip -c /var/lib/cwl/stge689bfd7-b21e-4aa9-81bd-02b92dbbfc34/GCF_024347215.1_ASM2434721v1_genomic.fna.gz | prodigal -d GCF_024347215.1_ASM2434721v1_genomic.fna/cds.fna -a GCF_024347215.1_ASM2434721v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:49,761] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:49,761] [INFO] Task started: HMMsearch
[2024-01-25 19:41:49,761] [INFO] Running command: hmmsearch --tblout GCF_024347215.1_ASM2434721v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5be61480-62a6-47e4-9811-689fa95841b0/dqc_reference/reference_markers.hmm GCF_024347215.1_ASM2434721v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:50,052] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:50,053] [INFO] Found 6/6 markers.
[2024-01-25 19:41:50,100] [INFO] Query marker FASTA was written to GCF_024347215.1_ASM2434721v1_genomic.fna/markers.fasta
[2024-01-25 19:41:50,100] [INFO] Task started: Blastn
[2024-01-25 19:41:50,100] [INFO] Running command: blastn -query GCF_024347215.1_ASM2434721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5be61480-62a6-47e4-9811-689fa95841b0/dqc_reference/reference_markers.fasta -out GCF_024347215.1_ASM2434721v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:50,696] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:50,699] [INFO] Selected 23 target genomes.
[2024-01-25 19:41:50,699] [INFO] Target genome list was writen to GCF_024347215.1_ASM2434721v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:50,721] [INFO] Task started: fastANI
[2024-01-25 19:41:50,721] [INFO] Running command: fastANI --query /var/lib/cwl/stge689bfd7-b21e-4aa9-81bd-02b92dbbfc34/GCF_024347215.1_ASM2434721v1_genomic.fna.gz --refList GCF_024347215.1_ASM2434721v1_genomic.fna/target_genomes.txt --output GCF_024347215.1_ASM2434721v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:07,098] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:07,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5be61480-62a6-47e4-9811-689fa95841b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:07,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5be61480-62a6-47e4-9811-689fa95841b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:07,107] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:07,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:07,107] [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 ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	100.0	1734	1737	95	conclusive
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	81.9342	1109	1737	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	78.6163	230	1737	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	78.5612	224	1737	95	below_threshold
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	78.5497	68	1737	95	below_threshold
Neptunomonas phycophila	strain=CECT 8716	GCA_001922575.1	1572645	1572645	type	True	78.4657	72	1737	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	78.4192	161	1737	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	78.1132	180	1737	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	78.0515	183	1737	95	below_threshold
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	77.6534	124	1737	95	below_threshold
Oceanospirillum linum	strain=ATCC 11336	GCA_001995095.2	966	966	type	True	76.4291	66	1737	95	below_threshold
Oceanospirillum beijerinckii	strain=DSM 7166	GCA_000422425.1	64976	64976	type	True	76.392	91	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:07,109] [INFO] DFAST Taxonomy check result was written to GCF_024347215.1_ASM2434721v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:07,109] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:07,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:07,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5be61480-62a6-47e4-9811-689fa95841b0/dqc_reference/checkm_data
[2024-01-25 19:42:07,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:07,159] [INFO] Task started: CheckM
[2024-01-25 19:42:07,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347215.1_ASM2434721v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347215.1_ASM2434721v1_genomic.fna/checkm_input GCF_024347215.1_ASM2434721v1_genomic.fna/checkm_result
[2024-01-25 19:42:48,822] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:48,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:48,840] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:48,840] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:48,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347215.1_ASM2434721v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:48,840] [INFO] Task started: Blastn
[2024-01-25 19:42:48,841] [INFO] Running command: blastn -query GCF_024347215.1_ASM2434721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5be61480-62a6-47e4-9811-689fa95841b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347215.1_ASM2434721v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:49,736] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:49,739] [INFO] Selected 19 target genomes.
[2024-01-25 19:42:49,739] [INFO] Target genome list was writen to GCF_024347215.1_ASM2434721v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:49,811] [INFO] Task started: fastANI
[2024-01-25 19:42:49,811] [INFO] Running command: fastANI --query /var/lib/cwl/stge689bfd7-b21e-4aa9-81bd-02b92dbbfc34/GCF_024347215.1_ASM2434721v1_genomic.fna.gz --refList GCF_024347215.1_ASM2434721v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347215.1_ASM2434721v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:02,699] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:02,708] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:43:02,708] [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_017051665.1	s__Amphritea spongicola	81.9342	1109	1737	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	80.2272	180	1737	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	78.6348	229	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018223185.1	s__Amphritea sp018223185	78.496	180	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCA_016744155.1	s__Amphritea sp016744155	78.4279	172	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957515.1	s__Amphritea opalescens	78.4158	160	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067325.1	s__Amphritea sp018067325	78.2162	124	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	-
GCF_900111095.1	s__Amphritea atlantica	78.1137	179	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924235.1	s__Amphritea sp016924235	78.1061	187	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCF_015209595.1	s__Pontibacterium sp015209595	77.8413	146	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pontibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435145.1	s__Neptuniibacter sp002435145	77.3449	75	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	99.91	99.87	0.93	0.93	3	-
GCF_000422425.1	s__Oceanospirillum beijerinckii	76.3865	88	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	98.77	98.77	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:02,710] [INFO] GTDB search result was written to GCF_024347215.1_ASM2434721v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:02,710] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:02,713] [INFO] DFAST_QC result json was written to GCF_024347215.1_ASM2434721v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:02,714] [INFO] DFAST_QC completed!
[2024-01-25 19:43:02,714] [INFO] Total running time: 0h1m27s