[2023-03-15 17:24:01,372] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,374] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg03afb8bf-f90c-4173-8c00-4eb08393304b/dqc_reference
[2023-03-15 17:24:02,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,649] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,650] [INFO] Running command: cat /var/lib/cwl/stgae389b90-7811-4c3d-9b33-cee5d209a355/OceanDNA-b34610.fa | prodigal -d OceanDNA-b34610/cds.fna -a OceanDNA-b34610/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:30,075] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:30,075] [INFO] Task started: HMMsearch
[2023-03-15 17:24:30,075] [INFO] Running command: hmmsearch --tblout OceanDNA-b34610/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03afb8bf-f90c-4173-8c00-4eb08393304b/dqc_reference/reference_markers.hmm OceanDNA-b34610/protein.faa > /dev/null
[2023-03-15 17:24:30,354] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:30,354] [INFO] Found 6/6 markers.
[2023-03-15 17:24:30,382] [INFO] Query marker FASTA was written to OceanDNA-b34610/markers.fasta
[2023-03-15 17:24:30,383] [INFO] Task started: Blastn
[2023-03-15 17:24:30,383] [INFO] Running command: blastn -query OceanDNA-b34610/markers.fasta -db /var/lib/cwl/stg03afb8bf-f90c-4173-8c00-4eb08393304b/dqc_reference/reference_markers.fasta -out OceanDNA-b34610/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:31,100] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:31,101] [INFO] Selected 26 target genomes.
[2023-03-15 17:24:31,102] [INFO] Target genome list was writen to OceanDNA-b34610/target_genomes.txt
[2023-03-15 17:24:31,121] [INFO] Task started: fastANI
[2023-03-15 17:24:31,121] [INFO] Running command: fastANI --query /var/lib/cwl/stgae389b90-7811-4c3d-9b33-cee5d209a355/OceanDNA-b34610.fa --refList OceanDNA-b34610/target_genomes.txt --output OceanDNA-b34610/fastani_result.tsv --threads 1
[2023-03-15 17:24:49,104] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:49,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03afb8bf-f90c-4173-8c00-4eb08393304b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:49,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03afb8bf-f90c-4173-8c00-4eb08393304b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:49,113] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 17:24:49,113] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 17:24:49,114] [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 confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	97.535	1358	1522	95	conclusive
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	78.8094	215	1522	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.2377	189	1522	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.1802	184	1522	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	78.0975	141	1522	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	77.9868	171	1522	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	77.9416	165	1522	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	77.919	214	1522	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	77.8608	214	1522	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	77.8221	151	1522	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	77.8122	202	1522	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	77.66	225	1522	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	77.4921	132	1522	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	76.6792	54	1522	95	below_threshold
Saliniradius amylolyticus	strain=HMF8227	GCA_003143555.1	2183582	2183582	type	True	76.605	60	1522	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:24:49,114] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34610/tc_result.tsv
[2023-03-15 17:24:49,114] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:49,114] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:49,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03afb8bf-f90c-4173-8c00-4eb08393304b/dqc_reference/checkm_data
[2023-03-15 17:24:49,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:49,121] [INFO] Task started: CheckM
[2023-03-15 17:24:49,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34610/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34610/checkm_input OceanDNA-b34610/checkm_result
[2023-03-15 17:25:54,985] [INFO] Task succeeded: CheckM
[2023-03-15 17:25:54,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:25:54,989] [INFO] ===== Completeness check finished =====
[2023-03-15 17:25:54,989] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:25:54,989] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34610/markers.fasta)
[2023-03-15 17:25:54,990] [INFO] Task started: Blastn
[2023-03-15 17:25:54,990] [INFO] Running command: blastn -query OceanDNA-b34610/markers.fasta -db /var/lib/cwl/stg03afb8bf-f90c-4173-8c00-4eb08393304b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34610/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:25:56,078] [INFO] Task succeeded: Blastn
[2023-03-15 17:25:56,079] [INFO] Selected 19 target genomes.
[2023-03-15 17:25:56,079] [INFO] Target genome list was writen to OceanDNA-b34610/target_genomes_gtdb.txt
[2023-03-15 17:25:56,107] [INFO] Task started: fastANI
[2023-03-15 17:25:56,108] [INFO] Running command: fastANI --query /var/lib/cwl/stgae389b90-7811-4c3d-9b33-cee5d209a355/OceanDNA-b34610.fa --refList OceanDNA-b34610/target_genomes_gtdb.txt --output OceanDNA-b34610/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:26:10,697] [INFO] Task succeeded: fastANI
[2023-03-15 17:26:10,709] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:26:10,709] [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_001757105.1	s__Alteromonas confluentis	97.5476	1357	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003584565.2	s__Alteromonas sp002729795	82.4272	638	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCA_019249295.1	s__Alteromonas antoniana	78.7971	215	1522	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	78.7872	181	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_018860965.1	s__Alteromonas sp018860965	78.6689	273	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860805.1	s__Alteromonas sp018860805	78.6664	282	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750655.1	s__Alteromonas profundi_A	78.4568	172	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808575.1	s__Alteromonas marina	78.4409	176	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_903772925.1	s__Alteromonas macleodii_A	78.3946	168	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129565.1	s__Alteromonas aggregata	78.2817	210	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	-
GCF_001953635.1	s__Alteromonas abrolhosensis	78.2102	182	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_000753865.1	s__Alteromonas sp000753865	78.1123	146	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010500865.1	s__Alteromonas profundi	78.088	140	1522	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	78.0233	168	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222225.1	s__Alteromonas lutimaris	77.8455	200	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	77.66	225	1522	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	77.5723	199	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCA_013373625.1	s__Alteromonas sp013373625	77.4565	136	1522	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	77.3267	225	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:26:10,709] [INFO] GTDB search result was written to OceanDNA-b34610/result_gtdb.tsv
[2023-03-15 17:26:10,709] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:26:10,711] [INFO] DFAST_QC result json was written to OceanDNA-b34610/dqc_result.json
[2023-03-15 17:26:10,711] [INFO] DFAST_QC completed!
[2023-03-15 17:26:10,711] [INFO] Total running time: 0h2m9s