[2023-03-18 04:04:53,860] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,861] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,861] [INFO] DQC Reference Directory: /var/lib/cwl/stg88a42639-b44b-486b-84f7-2f921079f152/dqc_reference
[2023-03-18 04:04:55,025] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,026] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,026] [INFO] Running command: cat /var/lib/cwl/stga4e643d9-c84d-4c69-ac0a-1fae2c9d9f38/OceanDNA-b34608.fa | prodigal -d OceanDNA-b34608/cds.fna -a OceanDNA-b34608/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:19,270] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:19,270] [INFO] Task started: HMMsearch
[2023-03-18 04:05:19,270] [INFO] Running command: hmmsearch --tblout OceanDNA-b34608/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88a42639-b44b-486b-84f7-2f921079f152/dqc_reference/reference_markers.hmm OceanDNA-b34608/protein.faa > /dev/null
[2023-03-18 04:05:19,498] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:19,499] [INFO] Found 6/6 markers.
[2023-03-18 04:05:19,525] [INFO] Query marker FASTA was written to OceanDNA-b34608/markers.fasta
[2023-03-18 04:05:19,526] [INFO] Task started: Blastn
[2023-03-18 04:05:19,526] [INFO] Running command: blastn -query OceanDNA-b34608/markers.fasta -db /var/lib/cwl/stg88a42639-b44b-486b-84f7-2f921079f152/dqc_reference/reference_markers.fasta -out OceanDNA-b34608/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:20,237] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:20,238] [INFO] Selected 17 target genomes.
[2023-03-18 04:05:20,238] [INFO] Target genome list was writen to OceanDNA-b34608/target_genomes.txt
[2023-03-18 04:05:20,250] [INFO] Task started: fastANI
[2023-03-18 04:05:20,250] [INFO] Running command: fastANI --query /var/lib/cwl/stga4e643d9-c84d-4c69-ac0a-1fae2c9d9f38/OceanDNA-b34608.fa --refList OceanDNA-b34608/target_genomes.txt --output OceanDNA-b34608/fastani_result.tsv --threads 1
[2023-03-18 04:05:34,251] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:34,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88a42639-b44b-486b-84f7-2f921079f152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:34,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88a42639-b44b-486b-84f7-2f921079f152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:34,259] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 04:05:34,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:05:34,260] [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	95.0952	1253	1416	95	conclusive
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	92.1393	1249	1416	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	81.1852	733	1416	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	81.1369	737	1416	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	79.5079	109	1416	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	78.4396	140	1416	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	77.7303	227	1416	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.4059	211	1416	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	77.2623	151	1416	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	77.2475	116	1416	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	77.2268	184	1416	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	76.2021	67	1416	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	75.8293	59	1416	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:05:34,260] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34608/tc_result.tsv
[2023-03-18 04:05:34,260] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:34,260] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:34,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88a42639-b44b-486b-84f7-2f921079f152/dqc_reference/checkm_data
[2023-03-18 04:05:34,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:34,266] [INFO] Task started: CheckM
[2023-03-18 04:05:34,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34608/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34608/checkm_input OceanDNA-b34608/checkm_result
[2023-03-18 04:06:34,471] [INFO] Task succeeded: CheckM
[2023-03-18 04:06:34,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.08%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:06:34,522] [INFO] ===== Completeness check finished =====
[2023-03-18 04:06:34,522] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:06:34,522] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34608/markers.fasta)
[2023-03-18 04:06:34,523] [INFO] Task started: Blastn
[2023-03-18 04:06:34,523] [INFO] Running command: blastn -query OceanDNA-b34608/markers.fasta -db /var/lib/cwl/stg88a42639-b44b-486b-84f7-2f921079f152/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34608/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:06:35,627] [INFO] Task succeeded: Blastn
[2023-03-18 04:06:35,629] [INFO] Selected 7 target genomes.
[2023-03-18 04:06:35,629] [INFO] Target genome list was writen to OceanDNA-b34608/target_genomes_gtdb.txt
[2023-03-18 04:06:35,817] [INFO] Task started: fastANI
[2023-03-18 04:06:35,817] [INFO] Running command: fastANI --query /var/lib/cwl/stga4e643d9-c84d-4c69-ac0a-1fae2c9d9f38/OceanDNA-b34608.fa --refList OceanDNA-b34608/target_genomes_gtdb.txt --output OceanDNA-b34608/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:06:43,620] [INFO] Task succeeded: fastANI
[2023-03-18 04:06:43,625] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 04:06:43,625] [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
GCA_002691625.1	s__Alteromonas sp002691625	99.2485	1135	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	inconclusive
GCF_002993365.1	s__Alteromonas alba	95.0817	1254	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002339125.1	s__Alteromonas sp002335925	92.9148	1126	1416	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	92.1393	1249	1416	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	90.9961	1264	1416	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	81.1819	733	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900129565.1	s__Alteromonas aggregata	79.0042	398	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	-
--------------------------------------------------------------------------------
[2023-03-18 04:06:43,625] [INFO] GTDB search result was written to OceanDNA-b34608/result_gtdb.tsv
[2023-03-18 04:06:43,626] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:06:43,627] [INFO] DFAST_QC result json was written to OceanDNA-b34608/dqc_result.json
[2023-03-18 04:06:43,627] [INFO] DFAST_QC completed!
[2023-03-18 04:06:43,627] [INFO] Total running time: 0h1m50s