[2024-01-24 13:58:42,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:42,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:42,216] [INFO] DQC Reference Directory: /var/lib/cwl/stge09db882-7013-4b1b-b014-e87b11299126/dqc_reference
[2024-01-24 13:58:43,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:43,553] [INFO] Task started: Prodigal
[2024-01-24 13:58:43,553] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f170f77-c14a-4296-92ea-93771f376414/GCF_002993365.1_ASM299336v1_genomic.fna.gz | prodigal -d GCF_002993365.1_ASM299336v1_genomic.fna/cds.fna -a GCF_002993365.1_ASM299336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:56,560] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:56,561] [INFO] Task started: HMMsearch
[2024-01-24 13:58:56,561] [INFO] Running command: hmmsearch --tblout GCF_002993365.1_ASM299336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge09db882-7013-4b1b-b014-e87b11299126/dqc_reference/reference_markers.hmm GCF_002993365.1_ASM299336v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:56,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:56,877] [INFO] Found 6/6 markers.
[2024-01-24 13:58:56,925] [INFO] Query marker FASTA was written to GCF_002993365.1_ASM299336v1_genomic.fna/markers.fasta
[2024-01-24 13:58:56,925] [INFO] Task started: Blastn
[2024-01-24 13:58:56,925] [INFO] Running command: blastn -query GCF_002993365.1_ASM299336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge09db882-7013-4b1b-b014-e87b11299126/dqc_reference/reference_markers.fasta -out GCF_002993365.1_ASM299336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:57,654] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:57,657] [INFO] Selected 18 target genomes.
[2024-01-24 13:58:57,657] [INFO] Target genome list was writen to GCF_002993365.1_ASM299336v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:57,664] [INFO] Task started: fastANI
[2024-01-24 13:58:57,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f170f77-c14a-4296-92ea-93771f376414/GCF_002993365.1_ASM299336v1_genomic.fna.gz --refList GCF_002993365.1_ASM299336v1_genomic.fna/target_genomes.txt --output GCF_002993365.1_ASM299336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:12,078] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:12,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge09db882-7013-4b1b-b014-e87b11299126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:12,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge09db882-7013-4b1b-b014-e87b11299126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:12,090] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:12,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:12,090] [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 alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	100.0	1601	1615	95	conclusive
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	93.7121	1340	1615	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	81.4434	780	1615	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	81.3993	784	1615	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	80.2277	269	1615	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	79.9016	168	1615	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	78.5218	235	1615	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	78.3524	122	1615	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	78.2914	169	1615	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	78.1327	128	1615	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.0031	219	1615	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.2343	65	1615	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	77.1764	78	1615	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:12,091] [INFO] DFAST Taxonomy check result was written to GCF_002993365.1_ASM299336v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:12,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:12,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:12,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge09db882-7013-4b1b-b014-e87b11299126/dqc_reference/checkm_data
[2024-01-24 13:59:12,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:12,140] [INFO] Task started: CheckM
[2024-01-24 13:59:12,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002993365.1_ASM299336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002993365.1_ASM299336v1_genomic.fna/checkm_input GCF_002993365.1_ASM299336v1_genomic.fna/checkm_result
[2024-01-24 13:59:51,422] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:51,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:51,445] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:51,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:51,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002993365.1_ASM299336v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:51,446] [INFO] Task started: Blastn
[2024-01-24 13:59:51,446] [INFO] Running command: blastn -query GCF_002993365.1_ASM299336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge09db882-7013-4b1b-b014-e87b11299126/dqc_reference/reference_markers_gtdb.fasta -out GCF_002993365.1_ASM299336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:52,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:52,382] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:52,382] [INFO] Target genome list was writen to GCF_002993365.1_ASM299336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:52,392] [INFO] Task started: fastANI
[2024-01-24 13:59:52,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f170f77-c14a-4296-92ea-93771f376414/GCF_002993365.1_ASM299336v1_genomic.fna.gz --refList GCF_002993365.1_ASM299336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002993365.1_ASM299336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:00,755] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:00,767] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:00,768] [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_002993365.1	s__Alteromonas alba	100.0	1601	1615	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_002691625.1	s__Alteromonas sp002691625	94.766	1085	1615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCA_002339125.1	s__Alteromonas sp002335925	94.4503	1196	1615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_003731635.1	s__Alteromonas oceani	93.721	1339	1615	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	91.7611	1303	1615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758465.1	s__Alteromonas lipolytica	81.4044	784	1615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:00,771] [INFO] GTDB search result was written to GCF_002993365.1_ASM299336v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:00,772] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:00,782] [INFO] DFAST_QC result json was written to GCF_002993365.1_ASM299336v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:00,782] [INFO] DFAST_QC completed!
[2024-01-24 14:00:00,782] [INFO] Total running time: 0h1m19s