[2024-01-24 10:57:12,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:12,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:12,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg24eeddb0-3341-4718-8a07-7856814f7a26/dqc_reference
[2024-01-24 10:57:14,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,012] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,012] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc7096f2-f04e-482e-afe2-28ba6852358b/GCF_024195295.1_ASM2419529v1_genomic.fna.gz | prodigal -d GCF_024195295.1_ASM2419529v1_genomic.fna/cds.fna -a GCF_024195295.1_ASM2419529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:25,331] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:25,331] [INFO] Task started: HMMsearch
[2024-01-24 10:57:25,332] [INFO] Running command: hmmsearch --tblout GCF_024195295.1_ASM2419529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24eeddb0-3341-4718-8a07-7856814f7a26/dqc_reference/reference_markers.hmm GCF_024195295.1_ASM2419529v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:25,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:25,624] [INFO] Found 6/6 markers.
[2024-01-24 10:57:25,657] [INFO] Query marker FASTA was written to GCF_024195295.1_ASM2419529v1_genomic.fna/markers.fasta
[2024-01-24 10:57:25,657] [INFO] Task started: Blastn
[2024-01-24 10:57:25,657] [INFO] Running command: blastn -query GCF_024195295.1_ASM2419529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24eeddb0-3341-4718-8a07-7856814f7a26/dqc_reference/reference_markers.fasta -out GCF_024195295.1_ASM2419529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:26,379] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:26,383] [INFO] Selected 22 target genomes.
[2024-01-24 10:57:26,384] [INFO] Target genome list was writen to GCF_024195295.1_ASM2419529v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:26,392] [INFO] Task started: fastANI
[2024-01-24 10:57:26,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7096f2-f04e-482e-afe2-28ba6852358b/GCF_024195295.1_ASM2419529v1_genomic.fna.gz --refList GCF_024195295.1_ASM2419529v1_genomic.fna/target_genomes.txt --output GCF_024195295.1_ASM2419529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:41,862] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:41,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24eeddb0-3341-4718-8a07-7856814f7a26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:41,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24eeddb0-3341-4718-8a07-7856814f7a26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:41,878] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:41,878] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:41,878] [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
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	81.6297	586	1305	95	below_threshold
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	77.7665	204	1305	95	below_threshold
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	77.4253	180	1305	95	below_threshold
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	77.169	187	1305	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	77.1399	168	1305	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	76.6937	103	1305	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	76.6864	132	1305	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	76.681	94	1305	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	76.6685	72	1305	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	76.4661	71	1305	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	76.4623	72	1305	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	76.3757	81	1305	95	below_threshold
Agaribacterium haliotis	strain=feces2	GCA_002312815.1	2013869	2013869	type	True	76.3636	66	1305	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2376	55	1305	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.9302	61	1305	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	75.8711	54	1305	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	75.8286	56	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:41,880] [INFO] DFAST Taxonomy check result was written to GCF_024195295.1_ASM2419529v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:41,881] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:41,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:41,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24eeddb0-3341-4718-8a07-7856814f7a26/dqc_reference/checkm_data
[2024-01-24 10:57:41,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:41,929] [INFO] Task started: CheckM
[2024-01-24 10:57:41,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024195295.1_ASM2419529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024195295.1_ASM2419529v1_genomic.fna/checkm_input GCF_024195295.1_ASM2419529v1_genomic.fna/checkm_result
[2024-01-24 10:58:17,416] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:17,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:17,434] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:17,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:17,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024195295.1_ASM2419529v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:17,436] [INFO] Task started: Blastn
[2024-01-24 10:58:17,436] [INFO] Running command: blastn -query GCF_024195295.1_ASM2419529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24eeddb0-3341-4718-8a07-7856814f7a26/dqc_reference/reference_markers_gtdb.fasta -out GCF_024195295.1_ASM2419529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:18,702] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:18,705] [INFO] Selected 18 target genomes.
[2024-01-24 10:58:18,705] [INFO] Target genome list was writen to GCF_024195295.1_ASM2419529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:18,747] [INFO] Task started: fastANI
[2024-01-24 10:58:18,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7096f2-f04e-482e-afe2-28ba6852358b/GCF_024195295.1_ASM2419529v1_genomic.fna.gz --refList GCF_024195295.1_ASM2419529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024195295.1_ASM2419529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:31,278] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:31,295] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:58:31,295] [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_000377745.1	s__Gilvimarinus chinensis	81.6418	585	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832015.1	s__Gilvimarinus agarilyticus	78.3421	405	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187555.1	s__Gilvimarinus polysaccharolyticus	77.7665	204	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750105.1	s__Microbulbifer aggregans	77.3727	72	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423345.1	s__Marinimicrobium agarilyticum	77.184	186	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259155.1	s__Marinimicrobium_A alkaliphilum	77.1399	168	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	76.8054	106	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182315.1	s__Cellvibrio polysaccharolyticus	76.701	130	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011440395.1	s__Pseudomaricurvus alcaniphilus	76.6959	104	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	98.35	98.35	0.88	0.88	2	-
GCF_001641755.2	s__Microbulbifer flavimaris	76.6739	70	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000019225.1	s__Cellvibrio japonicus	76.6394	116	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	100.00	100.00	1.00	1.00	4	-
GCF_011602085.1	s__Pseudoteredinibacter isoporae	76.4623	72	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudoteredinibacter	95.0	100.00	100.00	1.00	0.99	3	-
GCF_002312815.1	s__Agaribacterium haliotis	76.3924	65	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Agaribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953825.1	s__Cellvibrio sp000953825	76.359	93	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:31,296] [INFO] GTDB search result was written to GCF_024195295.1_ASM2419529v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:31,297] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:31,301] [INFO] DFAST_QC result json was written to GCF_024195295.1_ASM2419529v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:31,301] [INFO] DFAST_QC completed!
[2024-01-24 10:58:31,301] [INFO] Total running time: 0h1m19s