[2023-03-16 06:54:59,035] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:54:59,036] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:54:59,036] [INFO] DQC Reference Directory: /var/lib/cwl/stgb35e7cb5-3217-4af5-bf17-875cb5af3a92/dqc_reference
[2023-03-16 06:55:00,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:55:00,124] [INFO] Task started: Prodigal
[2023-03-16 06:55:00,124] [INFO] Running command: cat /var/lib/cwl/stg7ef263f6-96ef-480e-a71d-326219178d02/OceanDNA-b38943.fa | prodigal -d OceanDNA-b38943/cds.fna -a OceanDNA-b38943/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:55:08,039] [INFO] Task succeeded: Prodigal
[2023-03-16 06:55:08,039] [INFO] Task started: HMMsearch
[2023-03-16 06:55:08,039] [INFO] Running command: hmmsearch --tblout OceanDNA-b38943/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb35e7cb5-3217-4af5-bf17-875cb5af3a92/dqc_reference/reference_markers.hmm OceanDNA-b38943/protein.faa > /dev/null
[2023-03-16 06:55:08,207] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:55:08,208] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ef263f6-96ef-480e-a71d-326219178d02/OceanDNA-b38943.fa]
[2023-03-16 06:55:08,244] [INFO] Query marker FASTA was written to OceanDNA-b38943/markers.fasta
[2023-03-16 06:55:08,245] [INFO] Task started: Blastn
[2023-03-16 06:55:08,245] [INFO] Running command: blastn -query OceanDNA-b38943/markers.fasta -db /var/lib/cwl/stgb35e7cb5-3217-4af5-bf17-875cb5af3a92/dqc_reference/reference_markers.fasta -out OceanDNA-b38943/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:55:08,861] [INFO] Task succeeded: Blastn
[2023-03-16 06:55:08,865] [INFO] Selected 24 target genomes.
[2023-03-16 06:55:08,865] [INFO] Target genome list was writen to OceanDNA-b38943/target_genomes.txt
[2023-03-16 06:55:08,885] [INFO] Task started: fastANI
[2023-03-16 06:55:08,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ef263f6-96ef-480e-a71d-326219178d02/OceanDNA-b38943.fa --refList OceanDNA-b38943/target_genomes.txt --output OceanDNA-b38943/fastani_result.tsv --threads 1
[2023-03-16 06:55:22,806] [INFO] Task succeeded: fastANI
[2023-03-16 06:55:22,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb35e7cb5-3217-4af5-bf17-875cb5af3a92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:55:22,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb35e7cb5-3217-4af5-bf17-875cb5af3a92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:55:22,818] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:55:22,818] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:55:22,818] [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 bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	77.3838	103	365	95	below_threshold
Tamilnaduibacter salinus	strain=Mi-7	GCA_002287355.1	1484056	1484056	type	True	77.0628	56	365	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	77.0054	68	365	95	below_threshold
Marinobacter daqiaonensis	strain=YCSA40	GCA_012070355.1	650891	650891	type	True	76.9213	68	365	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	76.9096	87	365	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	76.891	81	365	95	below_threshold
Tamilnaduibacter salinus	strain=DSM 28688	GCA_003096655.1	1484056	1484056	type	True	76.8665	61	365	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	76.7397	67	365	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	76.4263	84	365	95	below_threshold
Marinobacter confluentis	strain=HJM-18	GCA_004785685.1	1697557	1697557	type	True	76.2882	51	365	95	below_threshold
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	76.2882	51	365	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	76.272	58	365	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	76.2697	58	365	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.2637	54	365	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.1624	55	365	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.0793	70	365	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:55:22,820] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38943/tc_result.tsv
[2023-03-16 06:55:22,822] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:55:22,822] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:55:22,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb35e7cb5-3217-4af5-bf17-875cb5af3a92/dqc_reference/checkm_data
[2023-03-16 06:55:22,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:55:22,827] [INFO] Task started: CheckM
[2023-03-16 06:55:22,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38943/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38943/checkm_input OceanDNA-b38943/checkm_result
[2023-03-16 06:55:47,751] [INFO] Task succeeded: CheckM
[2023-03-16 06:55:47,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:55:47,770] [INFO] ===== Completeness check finished =====
[2023-03-16 06:55:47,770] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:55:47,770] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38943/markers.fasta)
[2023-03-16 06:55:47,771] [INFO] Task started: Blastn
[2023-03-16 06:55:47,771] [INFO] Running command: blastn -query OceanDNA-b38943/markers.fasta -db /var/lib/cwl/stgb35e7cb5-3217-4af5-bf17-875cb5af3a92/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38943/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:55:48,782] [INFO] Task succeeded: Blastn
[2023-03-16 06:55:48,784] [INFO] Selected 14 target genomes.
[2023-03-16 06:55:48,784] [INFO] Target genome list was writen to OceanDNA-b38943/target_genomes_gtdb.txt
[2023-03-16 06:55:48,798] [INFO] Task started: fastANI
[2023-03-16 06:55:48,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ef263f6-96ef-480e-a71d-326219178d02/OceanDNA-b38943.fa --refList OceanDNA-b38943/target_genomes_gtdb.txt --output OceanDNA-b38943/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:55:56,587] [INFO] Task succeeded: fastANI
[2023-03-16 06:55:56,592] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:55:56,593] [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_900162675.1	s__Halospina utahensis_A	90.407	348	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856365.1	s__Halospina utahensis_B	90.1904	353	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	99.12	98.25	0.93	0.87	3	-
GCF_002286965.1	s__Halospina salipaludis	89.8627	358	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364635.1	s__Halospina denitrificans	79.1726	202	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007135745.1	s__Halospina sp007135745	77.1698	58	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651935.1	s__Marinobacter zhanjiangensis	77.0054	68	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789045.1	s__Marinobacter_A sp003789045	76.8398	93	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCF_001981305.1	s__Marinobacter lutaoensis	76.4263	84	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	-
--------------------------------------------------------------------------------
[2023-03-16 06:55:56,594] [INFO] GTDB search result was written to OceanDNA-b38943/result_gtdb.tsv
[2023-03-16 06:55:56,596] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:55:56,598] [INFO] DFAST_QC result json was written to OceanDNA-b38943/dqc_result.json
[2023-03-16 06:55:56,598] [INFO] DFAST_QC completed!
[2023-03-16 06:55:56,598] [INFO] Total running time: 0h0m58s