[2024-01-24 13:19:27,846] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:27,848] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:27,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e4cb9ad-ca7f-4a3b-806f-d86a195e6e74/dqc_reference
[2024-01-24 13:19:29,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:29,168] [INFO] Task started: Prodigal
[2024-01-24 13:19:29,168] [INFO] Running command: gunzip -c /var/lib/cwl/stgae73e8c2-d3b7-493e-b9f0-0b636a7df367/GCF_012295575.1_ASM1229557v1_genomic.fna.gz | prodigal -d GCF_012295575.1_ASM1229557v1_genomic.fna/cds.fna -a GCF_012295575.1_ASM1229557v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:40,266] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:40,267] [INFO] Task started: HMMsearch
[2024-01-24 13:19:40,267] [INFO] Running command: hmmsearch --tblout GCF_012295575.1_ASM1229557v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e4cb9ad-ca7f-4a3b-806f-d86a195e6e74/dqc_reference/reference_markers.hmm GCF_012295575.1_ASM1229557v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:40,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:40,563] [INFO] Found 6/6 markers.
[2024-01-24 13:19:40,603] [INFO] Query marker FASTA was written to GCF_012295575.1_ASM1229557v1_genomic.fna/markers.fasta
[2024-01-24 13:19:40,604] [INFO] Task started: Blastn
[2024-01-24 13:19:40,604] [INFO] Running command: blastn -query GCF_012295575.1_ASM1229557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4cb9ad-ca7f-4a3b-806f-d86a195e6e74/dqc_reference/reference_markers.fasta -out GCF_012295575.1_ASM1229557v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:41,463] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:41,467] [INFO] Selected 20 target genomes.
[2024-01-24 13:19:41,467] [INFO] Target genome list was writen to GCF_012295575.1_ASM1229557v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:41,507] [INFO] Task started: fastANI
[2024-01-24 13:19:41,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgae73e8c2-d3b7-493e-b9f0-0b636a7df367/GCF_012295575.1_ASM1229557v1_genomic.fna.gz --refList GCF_012295575.1_ASM1229557v1_genomic.fna/target_genomes.txt --output GCF_012295575.1_ASM1229557v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:58,274] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:58,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e4cb9ad-ca7f-4a3b-806f-d86a195e6e74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:58,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e4cb9ad-ca7f-4a3b-806f-d86a195e6e74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:58,285] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:58,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:58,285] [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 lipolytica	strain=S7	GCA_012295575.1	2724191	2724191	type	True	100.0	1375	1377	95	conclusive
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	80.2958	66	1377	95	below_threshold
Vibrio navarrensis	strain=ATCC 51183	GCA_000764325.1	29495	29495	type	True	79.1856	62	1377	95	below_threshold
Ferrimonas balearica	strain=DSM 9799	GCA_000148645.1	44012	44012	type	True	78.651	162	1377	95	below_threshold
Ferrimonas senticii	strain=DSM 18821	GCA_000422665.1	394566	394566	type	True	78.4987	313	1377	95	below_threshold
Ferrimonas aestuarii	strain=IMCC35002	GCA_005116665.1	2569539	2569539	type	True	77.9831	163	1377	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	77.7369	155	1377	95	below_threshold
Ferrimonas kyonanensis	strain=DSM 18153	GCA_000425405.1	364763	364763	type	True	77.5508	125	1377	95	below_threshold
Ferrimonas sediminum	strain=DSM 23317	GCA_900100175.1	718193	718193	type	True	77.4438	125	1377	95	below_threshold
Ferrimonas marina	strain=NBRC 102583	GCA_001571125.1	299255	299255	type	True	77.4089	144	1377	95	below_threshold
Paraferrimonas sedimenticola	strain=NBRC 101628	GCA_002282855.1	375674	375674	type	True	77.2719	71	1377	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.2557	56	1377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:58,287] [INFO] DFAST Taxonomy check result was written to GCF_012295575.1_ASM1229557v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:58,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:58,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:58,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e4cb9ad-ca7f-4a3b-806f-d86a195e6e74/dqc_reference/checkm_data
[2024-01-24 13:19:58,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:58,329] [INFO] Task started: CheckM
[2024-01-24 13:19:58,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012295575.1_ASM1229557v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012295575.1_ASM1229557v1_genomic.fna/checkm_input GCF_012295575.1_ASM1229557v1_genomic.fna/checkm_result
[2024-01-24 13:20:34,126] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:34,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:34,151] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:34,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:34,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012295575.1_ASM1229557v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:34,153] [INFO] Task started: Blastn
[2024-01-24 13:20:34,153] [INFO] Running command: blastn -query GCF_012295575.1_ASM1229557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4cb9ad-ca7f-4a3b-806f-d86a195e6e74/dqc_reference/reference_markers_gtdb.fasta -out GCF_012295575.1_ASM1229557v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:35,322] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:35,327] [INFO] Selected 20 target genomes.
[2024-01-24 13:20:35,327] [INFO] Target genome list was writen to GCF_012295575.1_ASM1229557v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:35,397] [INFO] Task started: fastANI
[2024-01-24 13:20:35,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgae73e8c2-d3b7-493e-b9f0-0b636a7df367/GCF_012295575.1_ASM1229557v1_genomic.fna.gz --refList GCF_012295575.1_ASM1229557v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012295575.1_ASM1229557v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:51,407] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:51,422] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:51,422] [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_012295575.1	s__Ferrimonas lipolytica	100.0	1375	1377	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_001482385.1	s__Pseudoalteromonas rubra_B	80.5152	57	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	95.23	95.23	0.89	0.89	2	-
GCF_000148645.1	s__Ferrimonas balearica	78.6597	161	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422665.1	s__Ferrimonas senticii	78.4956	311	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764325.1	s__Vibrio navarrensis	78.3427	58	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCF_005116665.1	s__Ferrimonas sp005116665	77.9973	161	1377	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	77.7369	155	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001559595.1	s__Enterovibrio coralii	77.626	55	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425405.1	s__Ferrimonas kyonanensis	77.5832	125	1377	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	77.408	124	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002282855.1	s__Paraferrimonas sedimenticola	77.272	71	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Paraferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026285.1	s__Photobacterium profundum	76.6637	56	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:51,424] [INFO] GTDB search result was written to GCF_012295575.1_ASM1229557v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:51,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:51,428] [INFO] DFAST_QC result json was written to GCF_012295575.1_ASM1229557v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:51,428] [INFO] DFAST_QC completed!
[2024-01-24 13:20:51,428] [INFO] Total running time: 0h1m24s