[2023-03-15 21:24:38,447] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:38,448] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:38,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg73642b24-3e88-4f5c-9d44-e79bd8b96f76/dqc_reference
[2023-03-15 21:24:39,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:39,590] [INFO] Task started: Prodigal
[2023-03-15 21:24:39,590] [INFO] Running command: cat /var/lib/cwl/stgfe6a2d18-49c7-4081-b4d5-f3ff34ac8e16/OceanDNA-b13081.fa | prodigal -d OceanDNA-b13081/cds.fna -a OceanDNA-b13081/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:56,743] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:56,743] [INFO] Task started: HMMsearch
[2023-03-15 21:24:56,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b13081/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73642b24-3e88-4f5c-9d44-e79bd8b96f76/dqc_reference/reference_markers.hmm OceanDNA-b13081/protein.faa > /dev/null
[2023-03-15 21:24:56,918] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:56,920] [INFO] Found 6/6 markers.
[2023-03-15 21:24:56,938] [INFO] Query marker FASTA was written to OceanDNA-b13081/markers.fasta
[2023-03-15 21:24:56,938] [INFO] Task started: Blastn
[2023-03-15 21:24:56,938] [INFO] Running command: blastn -query OceanDNA-b13081/markers.fasta -db /var/lib/cwl/stg73642b24-3e88-4f5c-9d44-e79bd8b96f76/dqc_reference/reference_markers.fasta -out OceanDNA-b13081/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:57,660] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:57,661] [INFO] Selected 25 target genomes.
[2023-03-15 21:24:57,661] [INFO] Target genome list was writen to OceanDNA-b13081/target_genomes.txt
[2023-03-15 21:24:57,674] [INFO] Task started: fastANI
[2023-03-15 21:24:57,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe6a2d18-49c7-4081-b4d5-f3ff34ac8e16/OceanDNA-b13081.fa --refList OceanDNA-b13081/target_genomes.txt --output OceanDNA-b13081/fastani_result.tsv --threads 1
[2023-03-15 21:25:15,409] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:15,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73642b24-3e88-4f5c-9d44-e79bd8b96f76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:25:15,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73642b24-3e88-4f5c-9d44-e79bd8b96f76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:25:15,420] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:25:15,420] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:25:15,421] [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
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	77.9404	327	608	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	77.8461	273	608	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.0364	113	608	95	below_threshold
Hymenobacter jeollabukensis	strain=1-3-3-8	GCA_005771675.1	2025313	2025313	type	True	75.0358	56	608	95	below_threshold
Glycomyces buryatensis	strain=18	GCA_004912275.1	2570927	2570927	type	True	74.983	63	608	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	74.903	72	608	95	below_threshold
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	74.889	91	608	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.8422	233	608	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	74.8373	127	608	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	74.8235	51	608	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	74.8071	75	608	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.806	164	608	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.8033	165	608	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	74.7746	61	608	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	74.7734	119	608	95	below_threshold
Glycomyces salinus	strain=YIM 93776	GCA_016428645.1	980294	980294	type	True	74.7685	79	608	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	74.7681	179	608	95	below_threshold
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	74.7337	69	608	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	74.7303	59	608	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:25:15,421] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13081/tc_result.tsv
[2023-03-15 21:25:15,421] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:25:15,421] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:25:15,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73642b24-3e88-4f5c-9d44-e79bd8b96f76/dqc_reference/checkm_data
[2023-03-15 21:25:15,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:25:15,552] [INFO] Task started: CheckM
[2023-03-15 21:25:15,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13081/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13081/checkm_input OceanDNA-b13081/checkm_result
[2023-03-15 21:25:59,065] [INFO] Task succeeded: CheckM
[2023-03-15 21:25:59,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.53%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 21:25:59,068] [INFO] ===== Completeness check finished =====
[2023-03-15 21:25:59,068] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:25:59,068] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13081/markers.fasta)
[2023-03-15 21:25:59,070] [INFO] Task started: Blastn
[2023-03-15 21:25:59,070] [INFO] Running command: blastn -query OceanDNA-b13081/markers.fasta -db /var/lib/cwl/stg73642b24-3e88-4f5c-9d44-e79bd8b96f76/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13081/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:26:00,322] [INFO] Task succeeded: Blastn
[2023-03-15 21:26:00,323] [INFO] Selected 10 target genomes.
[2023-03-15 21:26:00,323] [INFO] Target genome list was writen to OceanDNA-b13081/target_genomes_gtdb.txt
[2023-03-15 21:26:00,414] [INFO] Task started: fastANI
[2023-03-15 21:26:00,414] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe6a2d18-49c7-4081-b4d5-f3ff34ac8e16/OceanDNA-b13081.fa --refList OceanDNA-b13081/target_genomes_gtdb.txt --output OceanDNA-b13081/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:26:06,621] [INFO] Task succeeded: fastANI
[2023-03-15 21:26:06,626] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:26:06,627] [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_002283555.1	s__Rubrivirga sp002283555	78.8001	334	608	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCA_012960515.1	s__Rubricoccus sp012960515	78.0474	244	608	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283365.1	s__Rubrivirga marina	77.9243	330	608	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	77.8913	263	608	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	77.8116	276	608	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003465.1	s__JABDIZ01 sp013003465	77.3669	145	608	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	74.9102	72	608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302215.1	s__Dokdonella sp017302215	74.7292	79	608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381765.1	s__Gulosibacter faecalis	74.7207	73	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:26:06,627] [INFO] GTDB search result was written to OceanDNA-b13081/result_gtdb.tsv
[2023-03-15 21:26:06,627] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:26:06,628] [INFO] DFAST_QC result json was written to OceanDNA-b13081/dqc_result.json
[2023-03-15 21:26:06,629] [INFO] DFAST_QC completed!
[2023-03-15 21:26:06,629] [INFO] Total running time: 0h1m28s