[2024-01-24 12:07:06,703] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,705] [INFO] DQC Reference Directory: /var/lib/cwl/stg009c15c0-d4be-4e41-9af3-f696cb669175/dqc_reference
[2024-01-24 12:07:07,995] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,996] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,996] [INFO] Running command: gunzip -c /var/lib/cwl/stg8aed2f9e-e773-443c-9522-159f51402969/GCF_015644725.1_ASM1564472v1_genomic.fna.gz | prodigal -d GCF_015644725.1_ASM1564472v1_genomic.fna/cds.fna -a GCF_015644725.1_ASM1564472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:18,012] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:18,012] [INFO] Task started: HMMsearch
[2024-01-24 12:07:18,013] [INFO] Running command: hmmsearch --tblout GCF_015644725.1_ASM1564472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg009c15c0-d4be-4e41-9af3-f696cb669175/dqc_reference/reference_markers.hmm GCF_015644725.1_ASM1564472v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:18,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:18,346] [INFO] Found 6/6 markers.
[2024-01-24 12:07:18,387] [INFO] Query marker FASTA was written to GCF_015644725.1_ASM1564472v1_genomic.fna/markers.fasta
[2024-01-24 12:07:18,388] [INFO] Task started: Blastn
[2024-01-24 12:07:18,388] [INFO] Running command: blastn -query GCF_015644725.1_ASM1564472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg009c15c0-d4be-4e41-9af3-f696cb669175/dqc_reference/reference_markers.fasta -out GCF_015644725.1_ASM1564472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:19,080] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:19,085] [INFO] Selected 26 target genomes.
[2024-01-24 12:07:19,086] [INFO] Target genome list was writen to GCF_015644725.1_ASM1564472v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:19,096] [INFO] Task started: fastANI
[2024-01-24 12:07:19,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aed2f9e-e773-443c-9522-159f51402969/GCF_015644725.1_ASM1564472v1_genomic.fna.gz --refList GCF_015644725.1_ASM1564472v1_genomic.fna/target_genomes.txt --output GCF_015644725.1_ASM1564472v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:36,608] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:36,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg009c15c0-d4be-4e41-9af3-f696cb669175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:36,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg009c15c0-d4be-4e41-9af3-f696cb669175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:36,630] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:36,631] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:36,631] [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
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	79.2318	124	1255	95	below_threshold
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	79.1583	257	1255	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.8787	397	1255	95	below_threshold
Salinimonas chungwhensis	strain=DSM 16280	GCA_000378185.1	265425	265425	type	True	78.8192	278	1255	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	78.6268	142	1255	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	78.4893	284	1255	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.4847	123	1255	95	below_threshold
Alteromonas pelagimontana	strain=5.12	GCA_002499975.2	1858656	1858656	type	True	78.4581	170	1255	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	78.2215	174	1255	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	78.1639	140	1255	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	78.1629	117	1255	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	78.0105	179	1255	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	78.0041	207	1255	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	77.9167	182	1255	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	77.8341	168	1255	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.8068	214	1255	95	below_threshold
Alteromonas sediminis	strain=U0105	GCA_003820355.1	2259342	2259342	type	True	77.8064	69	1255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,633] [INFO] DFAST Taxonomy check result was written to GCF_015644725.1_ASM1564472v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:36,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:36,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:36,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg009c15c0-d4be-4e41-9af3-f696cb669175/dqc_reference/checkm_data
[2024-01-24 12:07:36,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:36,677] [INFO] Task started: CheckM
[2024-01-24 12:07:36,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015644725.1_ASM1564472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015644725.1_ASM1564472v1_genomic.fna/checkm_input GCF_015644725.1_ASM1564472v1_genomic.fna/checkm_result
[2024-01-24 12:08:10,892] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:10,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:10,916] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:10,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:10,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015644725.1_ASM1564472v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:10,917] [INFO] Task started: Blastn
[2024-01-24 12:08:10,917] [INFO] Running command: blastn -query GCF_015644725.1_ASM1564472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg009c15c0-d4be-4e41-9af3-f696cb669175/dqc_reference/reference_markers_gtdb.fasta -out GCF_015644725.1_ASM1564472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:11,818] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:11,824] [INFO] Selected 17 target genomes.
[2024-01-24 12:08:11,824] [INFO] Target genome list was writen to GCF_015644725.1_ASM1564472v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:11,833] [INFO] Task started: fastANI
[2024-01-24 12:08:11,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aed2f9e-e773-443c-9522-159f51402969/GCF_015644725.1_ASM1564472v1_genomic.fna.gz --refList GCF_015644725.1_ASM1564472v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015644725.1_ASM1564472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:24,030] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:24,047] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:24,047] [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_015644725.1	s__Alteromonas sp015644725	100.0	1255	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019249245.1	s__Alteromonas lipotrueiana	80.7247	656	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429285.1	s__Alteromonas sediminis	79.6793	453	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_006228385.1	s__Alteromonas iocasae	79.1033	257	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756315.1	s__Alteromonas sp009811495	78.8823	137	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.33	96.67	0.93	0.86	3	-
GCF_005222225.1	s__Alteromonas lutimaris	78.8595	396	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	78.8451	145	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005117025.1	s__Alteromonas portus	78.4804	124	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367475.1	s__Alteromonas aestuariivivens	78.043	177	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651815.1	s__Alteromonas halophila	77.9683	208	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003731635.1	s__Alteromonas oceani	77.918	182	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691625.1	s__Alteromonas sp002691625	77.8649	143	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_002993365.1	s__Alteromonas alba	77.8341	168	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222405.1	s__Alteromonas sp018222405	77.6371	168	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	77.4574	151	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:24,049] [INFO] GTDB search result was written to GCF_015644725.1_ASM1564472v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:24,050] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:24,055] [INFO] DFAST_QC result json was written to GCF_015644725.1_ASM1564472v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:24,056] [INFO] DFAST_QC completed!
[2024-01-24 12:08:24,056] [INFO] Total running time: 0h1m17s