[2023-03-16 10:35:15,179] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:35:15,179] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:35:15,179] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ce98a81-17a3-4a0f-a4e1-f38861fe9839/dqc_reference
[2023-03-16 10:35:16,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:35:16,277] [INFO] Task started: Prodigal
[2023-03-16 10:35:16,277] [INFO] Running command: cat /var/lib/cwl/stg74f1a640-494b-45fe-9abf-d5e859d084b5/OceanDNA-b34945.fa | prodigal -d OceanDNA-b34945/cds.fna -a OceanDNA-b34945/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:35:29,969] [INFO] Task succeeded: Prodigal
[2023-03-16 10:35:29,969] [INFO] Task started: HMMsearch
[2023-03-16 10:35:29,969] [INFO] Running command: hmmsearch --tblout OceanDNA-b34945/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ce98a81-17a3-4a0f-a4e1-f38861fe9839/dqc_reference/reference_markers.hmm OceanDNA-b34945/protein.faa > /dev/null
[2023-03-16 10:35:30,177] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:35:30,177] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg74f1a640-494b-45fe-9abf-d5e859d084b5/OceanDNA-b34945.fa]
[2023-03-16 10:35:30,200] [INFO] Query marker FASTA was written to OceanDNA-b34945/markers.fasta
[2023-03-16 10:35:30,201] [INFO] Task started: Blastn
[2023-03-16 10:35:30,201] [INFO] Running command: blastn -query OceanDNA-b34945/markers.fasta -db /var/lib/cwl/stg3ce98a81-17a3-4a0f-a4e1-f38861fe9839/dqc_reference/reference_markers.fasta -out OceanDNA-b34945/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:35:30,815] [INFO] Task succeeded: Blastn
[2023-03-16 10:35:30,816] [INFO] Selected 23 target genomes.
[2023-03-16 10:35:30,816] [INFO] Target genome list was writen to OceanDNA-b34945/target_genomes.txt
[2023-03-16 10:35:30,824] [INFO] Task started: fastANI
[2023-03-16 10:35:30,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg74f1a640-494b-45fe-9abf-d5e859d084b5/OceanDNA-b34945.fa --refList OceanDNA-b34945/target_genomes.txt --output OceanDNA-b34945/fastani_result.tsv --threads 1
[2023-03-16 10:35:45,667] [INFO] Task succeeded: fastANI
[2023-03-16 10:35:45,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ce98a81-17a3-4a0f-a4e1-f38861fe9839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:35:45,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ce98a81-17a3-4a0f-a4e1-f38861fe9839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:35:45,677] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:35:45,677] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:35:45,677] [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 phenolica	strain=O-BC30	GCA_004103265.1	161398	161398	suspected-type	True	80.3011	385	831	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	80.2686	404	831	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	80.2637	407	831	95	below_threshold
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	77.576	147	831	95	below_threshold
Pseudoalteromonas luteoviolacea	strain=CH130	GCA_014925325.1	43657	43657	suspected-type	True	77.559	130	831	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	77.5269	80	831	95	below_threshold
Pseudoalteromonas peptidolytica	strain=F12-50-A1	GCA_014858745.1	61150	61150	type	True	77.4846	127	831	95	below_threshold
Pseudoalteromonas caenipelagi	strain=JBTF-M23	GCA_013140855.1	2726988	2726988	type	True	77.4249	156	831	95	below_threshold
Pseudoalteromonas peptidolytica	strain=NBRC 101021	GCA_007989895.1	61150	61150	type	True	77.4126	115	831	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	77.3963	115	831	95	below_threshold
Pseudoalteromonas luteoviolacea	strain=DSM 6061	GCA_001625655.1	43657	43657	suspected-type	True	77.3461	129	831	95	below_threshold
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	77.3196	124	831	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	77.2768	109	831	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	77.2216	101	831	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	77.1357	109	831	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	76.9682	99	831	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.9633	101	831	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:35:45,678] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34945/tc_result.tsv
[2023-03-16 10:35:45,678] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:35:45,678] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:35:45,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ce98a81-17a3-4a0f-a4e1-f38861fe9839/dqc_reference/checkm_data
[2023-03-16 10:35:45,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:35:45,806] [INFO] Task started: CheckM
[2023-03-16 10:35:45,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34945/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34945/checkm_input OceanDNA-b34945/checkm_result
[2023-03-16 10:36:37,615] [INFO] Task succeeded: CheckM
[2023-03-16 10:36:37,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:36:37,617] [INFO] ===== Completeness check finished =====
[2023-03-16 10:36:37,617] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:36:37,618] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34945/markers.fasta)
[2023-03-16 10:36:37,619] [INFO] Task started: Blastn
[2023-03-16 10:36:37,619] [INFO] Running command: blastn -query OceanDNA-b34945/markers.fasta -db /var/lib/cwl/stg3ce98a81-17a3-4a0f-a4e1-f38861fe9839/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34945/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:36:38,902] [INFO] Task succeeded: Blastn
[2023-03-16 10:36:38,903] [INFO] Selected 21 target genomes.
[2023-03-16 10:36:38,903] [INFO] Target genome list was writen to OceanDNA-b34945/target_genomes_gtdb.txt
[2023-03-16 10:36:38,929] [INFO] Task started: fastANI
[2023-03-16 10:36:38,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg74f1a640-494b-45fe-9abf-d5e859d084b5/OceanDNA-b34945.fa --refList OceanDNA-b34945/target_genomes_gtdb.txt --output OceanDNA-b34945/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:37:02,273] [INFO] Task succeeded: fastANI
[2023-03-16 10:37:02,284] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:37:02,284] [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_005886345.1	s__Pseudoalteromonas phenolica_A	80.2757	441	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.97	0.91	0.89	3	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	80.2637	407	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_005876835.1	s__Pseudoalteromonas phenolica_B	80.1822	417	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814765.1	s__Pseudoalteromonas luteoviolacea_H	77.5323	124	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	95.23	95.23	0.92	0.92	2	-
GCA_000814675.1	s__Pseudoalteromonas distincta	77.5269	80	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_012641745.1	s__Pseudoalteromonas peptidolytica	77.4772	126	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.10	0.96	0.91	6	-
GCF_013140855.1	s__Pseudoalteromonas caenipelagi	77.4249	156	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	77.341	105	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_013391845.1	s__Pseudoalteromonas sp002685175	77.3349	93	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_002744175.1	s__Pseudoalteromonas piscicida_B	77.3128	117	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	77.2768	109	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_001750165.1	s__Pseudoalteromonas luteoviolacea_G	77.2403	127	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	99.99	1.00	1.00	5	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	77.1926	113	831	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	77.1357	109	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	-
GCF_001625695.1	s__Pseudoalteromonas luteoviolacea_B	77.1296	131	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.59	99.39	0.98	0.96	4	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	77.1262	110	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCF_001625565.1	s__Pseudoalteromonas luteoviolacea_F	77.0581	115	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002208135.1	s__Pseudoalteromonas piscicida_A	77.0338	122	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.45	98.90	0.97	0.95	3	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	77.0306	116	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_001469215.1	s__Pseudoalteromonas sp001469215	76.9081	101	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:37:02,298] [INFO] GTDB search result was written to OceanDNA-b34945/result_gtdb.tsv
[2023-03-16 10:37:02,298] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:37:02,301] [INFO] DFAST_QC result json was written to OceanDNA-b34945/dqc_result.json
[2023-03-16 10:37:02,301] [INFO] DFAST_QC completed!
[2023-03-16 10:37:02,301] [INFO] Total running time: 0h1m47s