[2023-03-15 17:39:54,920] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:39:54,920] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:39:54,920] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf83e5ed-5d1a-4d5c-8968-2e245cd10363/dqc_reference
[2023-03-15 17:39:57,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:39:57,554] [INFO] Task started: Prodigal
[2023-03-15 17:39:57,554] [INFO] Running command: cat /var/lib/cwl/stg8e4ef203-ea95-42e6-b5b6-6666fbc9155f/OceanDNA-b23834.fa | prodigal -d OceanDNA-b23834/cds.fna -a OceanDNA-b23834/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:40:14,784] [INFO] Task succeeded: Prodigal
[2023-03-15 17:40:14,784] [INFO] Task started: HMMsearch
[2023-03-15 17:40:14,785] [INFO] Running command: hmmsearch --tblout OceanDNA-b23834/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf83e5ed-5d1a-4d5c-8968-2e245cd10363/dqc_reference/reference_markers.hmm OceanDNA-b23834/protein.faa > /dev/null
[2023-03-15 17:40:14,970] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:40:14,970] [INFO] Found 6/6 markers.
[2023-03-15 17:40:14,989] [INFO] Query marker FASTA was written to OceanDNA-b23834/markers.fasta
[2023-03-15 17:40:14,989] [INFO] Task started: Blastn
[2023-03-15 17:40:14,989] [INFO] Running command: blastn -query OceanDNA-b23834/markers.fasta -db /var/lib/cwl/stgaf83e5ed-5d1a-4d5c-8968-2e245cd10363/dqc_reference/reference_markers.fasta -out OceanDNA-b23834/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:40:15,826] [INFO] Task succeeded: Blastn
[2023-03-15 17:40:15,827] [INFO] Selected 22 target genomes.
[2023-03-15 17:40:15,828] [INFO] Target genome list was writen to OceanDNA-b23834/target_genomes.txt
[2023-03-15 17:40:15,841] [INFO] Task started: fastANI
[2023-03-15 17:40:15,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4ef203-ea95-42e6-b5b6-6666fbc9155f/OceanDNA-b23834.fa --refList OceanDNA-b23834/target_genomes.txt --output OceanDNA-b23834/fastani_result.tsv --threads 1
[2023-03-15 17:40:29,866] [INFO] Task succeeded: fastANI
[2023-03-15 17:40:29,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf83e5ed-5d1a-4d5c-8968-2e245cd10363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:40:29,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf83e5ed-5d1a-4d5c-8968-2e245cd10363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:40:29,880] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:40:29,880] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:40:29,880] [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
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	79.2149	433	920	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	79.1727	484	920	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	78.593	393	920	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.2316	182	920	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.2159	183	920	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.1635	193	920	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.0809	194	920	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.0724	190	920	95	below_threshold
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	76.8452	158	920	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.7764	74	920	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	76.7456	75	920	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.7388	75	920	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	76.3365	71	920	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	76.0636	74	920	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.0333	73	920	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	75.9979	81	920	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	75.9677	83	920	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	75.7495	82	920	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.7394	73	920	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	75.6579	56	920	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.4203	54	920	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:40:29,880] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23834/tc_result.tsv
[2023-03-15 17:40:29,880] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:40:29,880] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:40:29,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf83e5ed-5d1a-4d5c-8968-2e245cd10363/dqc_reference/checkm_data
[2023-03-15 17:40:29,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:40:30,002] [INFO] Task started: CheckM
[2023-03-15 17:40:30,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23834/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23834/checkm_input OceanDNA-b23834/checkm_result
[2023-03-15 17:41:14,986] [INFO] Task succeeded: CheckM
[2023-03-15 17:41:14,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:41:14,989] [INFO] ===== Completeness check finished =====
[2023-03-15 17:41:14,989] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:41:14,989] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23834/markers.fasta)
[2023-03-15 17:41:14,991] [INFO] Task started: Blastn
[2023-03-15 17:41:14,991] [INFO] Running command: blastn -query OceanDNA-b23834/markers.fasta -db /var/lib/cwl/stgaf83e5ed-5d1a-4d5c-8968-2e245cd10363/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23834/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:41:16,641] [INFO] Task succeeded: Blastn
[2023-03-15 17:41:16,642] [INFO] Selected 15 target genomes.
[2023-03-15 17:41:16,642] [INFO] Target genome list was writen to OceanDNA-b23834/target_genomes_gtdb.txt
[2023-03-15 17:41:16,946] [INFO] Task started: fastANI
[2023-03-15 17:41:16,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4ef203-ea95-42e6-b5b6-6666fbc9155f/OceanDNA-b23834.fa --refList OceanDNA-b23834/target_genomes_gtdb.txt --output OceanDNA-b23834/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:41:26,030] [INFO] Task succeeded: fastANI
[2023-03-15 17:41:26,039] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:41:26,039] [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_017643585.1	s__Maricaulis sp017643585	79.7719	469	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.94	99.90	0.97	0.94	3	-
GCA_017643475.1	s__Maricaulis sp017643475	79.5244	475	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	79.334	460	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	79.2147	433	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_016817355.1	s__Maricaulis parjimensis	79.2119	454	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871165.1	s__Maricaulis sp005871165	79.1727	484	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665295.1	s__Maricaulis sp015665295	78.9415	445	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694345.1	s__Maricaulis sp002694345	78.7395	308	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480005.1	s__Maricaulis sp905480005	78.6385	403	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222865.1	s__Maricaulis sp018222865	78.6241	393	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420265.1	s__Oceanicaulis alexandrii	77.1446	177	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	-
GCA_017418605.1	s__CAISGS01 sp017418605	76.2259	117	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016201015.1	s__JACQDQ01 sp016201015	75.2963	59	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQDQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:41:26,039] [INFO] GTDB search result was written to OceanDNA-b23834/result_gtdb.tsv
[2023-03-15 17:41:26,039] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:41:26,041] [INFO] DFAST_QC result json was written to OceanDNA-b23834/dqc_result.json
[2023-03-15 17:41:26,041] [INFO] DFAST_QC completed!
[2023-03-15 17:41:26,041] [INFO] Total running time: 0h1m31s