[2023-03-17 05:26:45,853] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,853] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,853] [INFO] DQC Reference Directory: /var/lib/cwl/stgd86c95d6-246f-4ddd-ab71-537c51aabb5f/dqc_reference
[2023-03-17 05:26:47,031] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:47,031] [INFO] Task started: Prodigal
[2023-03-17 05:26:47,031] [INFO] Running command: cat /var/lib/cwl/stg57abd9ef-7645-4591-9bab-65d4c9ecf801/OceanDNA-b36084.fa | prodigal -d OceanDNA-b36084/cds.fna -a OceanDNA-b36084/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:27:09,140] [INFO] Task succeeded: Prodigal
[2023-03-17 05:27:09,140] [INFO] Task started: HMMsearch
[2023-03-17 05:27:09,140] [INFO] Running command: hmmsearch --tblout OceanDNA-b36084/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd86c95d6-246f-4ddd-ab71-537c51aabb5f/dqc_reference/reference_markers.hmm OceanDNA-b36084/protein.faa > /dev/null
[2023-03-17 05:27:09,340] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:27:09,341] [INFO] Found 6/6 markers.
[2023-03-17 05:27:09,362] [INFO] Query marker FASTA was written to OceanDNA-b36084/markers.fasta
[2023-03-17 05:27:09,363] [INFO] Task started: Blastn
[2023-03-17 05:27:09,363] [INFO] Running command: blastn -query OceanDNA-b36084/markers.fasta -db /var/lib/cwl/stgd86c95d6-246f-4ddd-ab71-537c51aabb5f/dqc_reference/reference_markers.fasta -out OceanDNA-b36084/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:10,111] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:10,112] [INFO] Selected 24 target genomes.
[2023-03-17 05:27:10,112] [INFO] Target genome list was writen to OceanDNA-b36084/target_genomes.txt
[2023-03-17 05:27:10,123] [INFO] Task started: fastANI
[2023-03-17 05:27:10,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg57abd9ef-7645-4591-9bab-65d4c9ecf801/OceanDNA-b36084.fa --refList OceanDNA-b36084/target_genomes.txt --output OceanDNA-b36084/fastani_result.tsv --threads 1
[2023-03-17 05:27:26,612] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:26,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd86c95d6-246f-4ddd-ab71-537c51aabb5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:27:26,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd86c95d6-246f-4ddd-ab71-537c51aabb5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:27:26,626] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:27:26,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:27:26,627] [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
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	81.6488	698	1143	95	below_threshold
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	78.2198	309	1143	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	78.1611	358	1143	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	78.0726	132	1143	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.0493	99	1143	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	78.0473	283	1143	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	77.8642	277	1143	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	77.7053	299	1143	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	77.6517	208	1143	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.6313	108	1143	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	77.531	287	1143	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	77.419	236	1143	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	77.2258	234	1143	95	below_threshold
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	77.2072	201	1143	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	77.0792	136	1143	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.5935	128	1143	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	76.5531	103	1143	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	76.4751	144	1143	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.4085	88	1143	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.3193	135	1143	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.1484	93	1143	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.1416	87	1143	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.0951	101	1143	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	75.7907	79	1143	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:27:26,627] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36084/tc_result.tsv
[2023-03-17 05:27:26,627] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:27:26,627] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:27:26,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd86c95d6-246f-4ddd-ab71-537c51aabb5f/dqc_reference/checkm_data
[2023-03-17 05:27:26,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:27:26,648] [INFO] Task started: CheckM
[2023-03-17 05:27:26,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36084/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36084/checkm_input OceanDNA-b36084/checkm_result
[2023-03-17 05:28:30,934] [INFO] Task succeeded: CheckM
[2023-03-17 05:28:30,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:28:30,937] [INFO] ===== Completeness check finished =====
[2023-03-17 05:28:30,937] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:28:30,938] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36084/markers.fasta)
[2023-03-17 05:28:30,938] [INFO] Task started: Blastn
[2023-03-17 05:28:30,938] [INFO] Running command: blastn -query OceanDNA-b36084/markers.fasta -db /var/lib/cwl/stgd86c95d6-246f-4ddd-ab71-537c51aabb5f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36084/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:28:32,313] [INFO] Task succeeded: Blastn
[2023-03-17 05:28:32,314] [INFO] Selected 21 target genomes.
[2023-03-17 05:28:32,315] [INFO] Target genome list was writen to OceanDNA-b36084/target_genomes_gtdb.txt
[2023-03-17 05:28:32,624] [INFO] Task started: fastANI
[2023-03-17 05:28:32,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg57abd9ef-7645-4591-9bab-65d4c9ecf801/OceanDNA-b36084.fa --refList OceanDNA-b36084/target_genomes_gtdb.txt --output OceanDNA-b36084/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:28:46,744] [INFO] Task succeeded: fastANI
[2023-03-17 05:28:46,756] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:28:46,757] [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_016918765.1	s__Polycyclovorans sp016918765	81.6406	698	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706265.1	s__Polycyclovorans sp002706265	78.7929	329	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	99.22	98.54	0.87	0.78	3	-
GCF_003428335.1	s__Solimonas_A sp003428335	78.3006	346	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711245.1	s__Polycyclovorans algicola	78.2199	309	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	78.2173	305	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	78.1714	357	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730135.1	s__Stagnimonas aquatica	78.1283	313	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	78.0224	285	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297005.1	s__Stagnimonas sp004297005	77.8641	281	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
GCF_000474945.1	s__Solimonas soli	77.8522	276	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	77.761	277	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182805.1	s__JACPFV01 sp016182805	77.6783	165	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__JACPFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010092425.1	s__Sinimarinibacterium sp010092425	77.6082	144	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	77.5528	285	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	77.4074	237	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	77.2169	233	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129825.1	s__Hydrocarboniphaga daqingensis	77.2072	201	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	77.0262	86	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943415.1	s__Perlucidibaca sp002943415	76.7032	94	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	76.3058	89	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	75.9799	101	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:28:46,757] [INFO] GTDB search result was written to OceanDNA-b36084/result_gtdb.tsv
[2023-03-17 05:28:46,758] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:28:46,760] [INFO] DFAST_QC result json was written to OceanDNA-b36084/dqc_result.json
[2023-03-17 05:28:46,760] [INFO] DFAST_QC completed!
[2023-03-17 05:28:46,760] [INFO] Total running time: 0h2m1s