[2023-03-14 10:55:58,905] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,906] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,906] [INFO] DQC Reference Directory: /var/lib/cwl/stgea0b65be-2371-446e-95b7-b9b2d8fcfbe1/dqc_reference
[2023-03-14 10:56:00,679] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,680] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,680] [INFO] Running command: cat /var/lib/cwl/stg68114a6c-14c6-4f8e-80f4-7d852d841be6/OceanDNA-b39114.fa | prodigal -d OceanDNA-b39114/cds.fna -a OceanDNA-b39114/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:24,072] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:24,073] [INFO] Task started: HMMsearch
[2023-03-14 10:56:24,073] [INFO] Running command: hmmsearch --tblout OceanDNA-b39114/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea0b65be-2371-446e-95b7-b9b2d8fcfbe1/dqc_reference/reference_markers.hmm OceanDNA-b39114/protein.faa > /dev/null
[2023-03-14 10:56:24,408] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:24,409] [INFO] Found 6/6 markers.
[2023-03-14 10:56:24,434] [INFO] Query marker FASTA was written to OceanDNA-b39114/markers.fasta
[2023-03-14 10:56:24,434] [INFO] Task started: Blastn
[2023-03-14 10:56:24,434] [INFO] Running command: blastn -query OceanDNA-b39114/markers.fasta -db /var/lib/cwl/stgea0b65be-2371-446e-95b7-b9b2d8fcfbe1/dqc_reference/reference_markers.fasta -out OceanDNA-b39114/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:25,151] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:25,152] [INFO] Selected 22 target genomes.
[2023-03-14 10:56:25,152] [INFO] Target genome list was writen to OceanDNA-b39114/target_genomes.txt
[2023-03-14 10:56:25,165] [INFO] Task started: fastANI
[2023-03-14 10:56:25,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg68114a6c-14c6-4f8e-80f4-7d852d841be6/OceanDNA-b39114.fa --refList OceanDNA-b39114/target_genomes.txt --output OceanDNA-b39114/fastani_result.tsv --threads 1
[2023-03-14 10:56:43,306] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:43,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea0b65be-2371-446e-95b7-b9b2d8fcfbe1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:43,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea0b65be-2371-446e-95b7-b9b2d8fcfbe1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:43,318] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 10:56:43,319] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 10:56:43,319] [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
Marinobacter segnicrescens	strain=CGMCC 1.6489	GCA_900111555.1	430453	430453	type	True	98.4949	1120	1240	95	conclusive
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	87.2688	938	1240	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	81.1403	721	1240	95	below_threshold
Marinobacter daqiaonensis	strain=CGMCC 1.9167	GCA_900115285.1	650891	650891	type	True	80.1964	589	1240	95	below_threshold
Marinobacter daqiaonensis	strain=YCSA40	GCA_012070355.1	650891	650891	type	True	80.1918	590	1240	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	79.2997	397	1240	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.2599	403	1240	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.9091	327	1240	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	78.8944	364	1240	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	78.4607	340	1240	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.441	341	1240	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	78.3549	318	1240	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.3503	318	1240	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	78.347	346	1240	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	78.246	329	1240	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.2246	324	1240	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	78.1109	317	1240	95	below_threshold
Marinobacter nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	77.8944	273	1240	95	below_threshold
Marinobacter mobilis	strain=CGMCC 1.7059	GCA_900106945.1	488533	488533	type	True	77.7037	278	1240	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	76.3171	91	1240	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.82	54	1240	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:43,319] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39114/tc_result.tsv
[2023-03-14 10:56:43,319] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:43,319] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:43,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea0b65be-2371-446e-95b7-b9b2d8fcfbe1/dqc_reference/checkm_data
[2023-03-14 10:56:43,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:43,411] [INFO] Task started: CheckM
[2023-03-14 10:56:43,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39114/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39114/checkm_input OceanDNA-b39114/checkm_result
[2023-03-14 10:57:40,721] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:40,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.88%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:40,724] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:40,725] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:40,725] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39114/markers.fasta)
[2023-03-14 10:57:40,725] [INFO] Task started: Blastn
[2023-03-14 10:57:40,725] [INFO] Running command: blastn -query OceanDNA-b39114/markers.fasta -db /var/lib/cwl/stgea0b65be-2371-446e-95b7-b9b2d8fcfbe1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39114/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:41,931] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:41,932] [INFO] Selected 25 target genomes.
[2023-03-14 10:57:41,932] [INFO] Target genome list was writen to OceanDNA-b39114/target_genomes_gtdb.txt
[2023-03-14 10:57:41,953] [INFO] Task started: fastANI
[2023-03-14 10:57:41,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg68114a6c-14c6-4f8e-80f4-7d852d841be6/OceanDNA-b39114.fa --refList OceanDNA-b39114/target_genomes_gtdb.txt --output OceanDNA-b39114/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:59,524] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:59,538] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:59,539] [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_900111555.1	s__Marinobacter segnicrescens	98.514	1119	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014651935.1	s__Marinobacter zhanjiangensis	81.1495	720	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115285.1	s__Marinobacter daqiaonensis	80.2058	588	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900114925.1	s__Marinobacter pelagius	79.2986	396	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	79.248	404	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_003315345.1	s__Marinobacter pelagius_A	79.1335	407	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934325.1	s__Marinobacter persicus_A	79.1301	348	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCA_014359475.1	s__Marinobacter sp014359475	78.9121	350	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	78.8944	364	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000831005.1	s__Marinobacter salarius	78.8068	325	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.84	96.73	0.88	0.79	21	-
GCF_003994855.1	s__Marinobacter sp003994855	78.7374	347	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	78.6718	289	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643965.1	s__Marinobacter sp017643965	78.5881	277	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617755.1	s__Marinobacter salsuginis	78.5732	346	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
GCF_002933295.1	s__Marinobacter flavimaris	78.5286	333	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_001981305.1	s__Marinobacter lutaoensis	78.461	339	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	-
GCF_003441595.1	s__Marinobacter sp003441595	78.4088	346	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201735.1	s__Marinobacter oulmenensis	78.3502	345	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347775.1	s__Marinobacter santoriniensis	78.3388	317	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327985.1	s__Marinobacter_A halodurans	78.246	329	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170835.1	s__Marinobacter algicola	78.1109	317	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301335.1	s__Marinobacter sp017301335	77.9921	268	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708045.1	s__Marinobacter nitratireducens	77.8992	272	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.86	98.83	0.90	0.89	3	-
GCA_002726615.1	s__Marinobacter sp002726615	77.8092	220	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.30	0.75	0.64	3	-
GCF_900106945.1	s__Marinobacter mobilis	77.7102	278	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:59,539] [INFO] GTDB search result was written to OceanDNA-b39114/result_gtdb.tsv
[2023-03-14 10:57:59,539] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:59,541] [INFO] DFAST_QC result json was written to OceanDNA-b39114/dqc_result.json
[2023-03-14 10:57:59,542] [INFO] DFAST_QC completed!
[2023-03-14 10:57:59,542] [INFO] Total running time: 0h2m1s