[2023-03-15 08:12:33,752] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:12:33,753] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:12:33,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f490971-91e5-436b-a889-12f38a47f5f9/dqc_reference
[2023-03-15 08:12:34,926] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:12:34,926] [INFO] Task started: Prodigal
[2023-03-15 08:12:34,926] [INFO] Running command: cat /var/lib/cwl/stgab4b5b73-ab5e-4098-ba4f-4299ef903c76/OceanDNA-b35016.fa | prodigal -d OceanDNA-b35016/cds.fna -a OceanDNA-b35016/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:12:58,758] [INFO] Task succeeded: Prodigal
[2023-03-15 08:12:58,759] [INFO] Task started: HMMsearch
[2023-03-15 08:12:58,759] [INFO] Running command: hmmsearch --tblout OceanDNA-b35016/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f490971-91e5-436b-a889-12f38a47f5f9/dqc_reference/reference_markers.hmm OceanDNA-b35016/protein.faa > /dev/null
[2023-03-15 08:12:59,005] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:12:59,005] [INFO] Found 6/6 markers.
[2023-03-15 08:12:59,042] [INFO] Query marker FASTA was written to OceanDNA-b35016/markers.fasta
[2023-03-15 08:12:59,043] [INFO] Task started: Blastn
[2023-03-15 08:12:59,043] [INFO] Running command: blastn -query OceanDNA-b35016/markers.fasta -db /var/lib/cwl/stg5f490971-91e5-436b-a889-12f38a47f5f9/dqc_reference/reference_markers.fasta -out OceanDNA-b35016/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:12:59,760] [INFO] Task succeeded: Blastn
[2023-03-15 08:12:59,767] [INFO] Selected 11 target genomes.
[2023-03-15 08:12:59,767] [INFO] Target genome list was writen to OceanDNA-b35016/target_genomes.txt
[2023-03-15 08:12:59,800] [INFO] Task started: fastANI
[2023-03-15 08:12:59,800] [INFO] Running command: fastANI --query /var/lib/cwl/stgab4b5b73-ab5e-4098-ba4f-4299ef903c76/OceanDNA-b35016.fa --refList OceanDNA-b35016/target_genomes.txt --output OceanDNA-b35016/fastani_result.tsv --threads 1
[2023-03-15 08:13:09,284] [INFO] Task succeeded: fastANI
[2023-03-15 08:13:09,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f490971-91e5-436b-a889-12f38a47f5f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:13:09,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f490971-91e5-436b-a889-12f38a47f5f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:13:09,292] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 08:13:09,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 08:13:09,292] [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
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	98.883	1292	1456	95	conclusive
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	98.8497	1304	1456	95	conclusive
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	83.9066	1047	1456	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	83.8912	1026	1456	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	83.8856	1052	1456	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	83.411	940	1456	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	78.8607	99	1456	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	76.6784	65	1456	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	76.2924	65	1456	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	75.7833	69	1456	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:13:09,298] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35016/tc_result.tsv
[2023-03-15 08:13:09,298] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:13:09,299] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:13:09,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f490971-91e5-436b-a889-12f38a47f5f9/dqc_reference/checkm_data
[2023-03-15 08:13:09,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:13:09,311] [INFO] Task started: CheckM
[2023-03-15 08:13:09,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35016/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35016/checkm_input OceanDNA-b35016/checkm_result
[2023-03-15 08:14:08,365] [INFO] Task succeeded: CheckM
[2023-03-15 08:14:08,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:14:08,399] [INFO] ===== Completeness check finished =====
[2023-03-15 08:14:08,399] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:14:08,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35016/markers.fasta)
[2023-03-15 08:14:08,400] [INFO] Task started: Blastn
[2023-03-15 08:14:08,400] [INFO] Running command: blastn -query OceanDNA-b35016/markers.fasta -db /var/lib/cwl/stg5f490971-91e5-436b-a889-12f38a47f5f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35016/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:14:09,823] [INFO] Task succeeded: Blastn
[2023-03-15 08:14:09,829] [INFO] Selected 10 target genomes.
[2023-03-15 08:14:09,829] [INFO] Target genome list was writen to OceanDNA-b35016/target_genomes_gtdb.txt
[2023-03-15 08:14:09,841] [INFO] Task started: fastANI
[2023-03-15 08:14:09,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgab4b5b73-ab5e-4098-ba4f-4299ef903c76/OceanDNA-b35016.fa --refList OceanDNA-b35016/target_genomes_gtdb.txt --output OceanDNA-b35016/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:14:19,682] [INFO] Task succeeded: fastANI
[2023-03-15 08:14:19,689] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:14:19,689] [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_900116435.1	s__Pseudoalteromonas lipolytica	98.8638	1294	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	conclusive
GCF_013391845.1	s__Pseudoalteromonas sp002685175	83.9677	836	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	83.9003	1025	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	83.8982	1050	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_013349995.1	s__Pseudoalteromonas sp013349995	83.8776	1006	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.6093	97.46	97.37	0.85	0.84	6	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	83.6835	985	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	83.6358	1030	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	83.5881	974	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	83.5448	996	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_001550155.1	s__Pseudoalteromonas arabiensis	83.411	940	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-15 08:14:19,693] [INFO] GTDB search result was written to OceanDNA-b35016/result_gtdb.tsv
[2023-03-15 08:14:19,697] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:14:19,702] [INFO] DFAST_QC result json was written to OceanDNA-b35016/dqc_result.json
[2023-03-15 08:14:19,703] [INFO] DFAST_QC completed!
[2023-03-15 08:14:19,703] [INFO] Total running time: 0h1m46s