[2023-03-15 03:51:12,268] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:51:12,268] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:51:12,268] [INFO] DQC Reference Directory: /var/lib/cwl/stge6c704df-f4bf-42be-838d-37019928ec14/dqc_reference
[2023-03-15 03:51:13,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:51:13,358] [INFO] Task started: Prodigal
[2023-03-15 03:51:13,358] [INFO] Running command: cat /var/lib/cwl/stg62b710f9-8dd4-444b-a85a-7bddb0f6fa7d/OceanDNA-b13091.fa | prodigal -d OceanDNA-b13091/cds.fna -a OceanDNA-b13091/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:51:27,642] [INFO] Task succeeded: Prodigal
[2023-03-15 03:51:27,642] [INFO] Task started: HMMsearch
[2023-03-15 03:51:27,642] [INFO] Running command: hmmsearch --tblout OceanDNA-b13091/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6c704df-f4bf-42be-838d-37019928ec14/dqc_reference/reference_markers.hmm OceanDNA-b13091/protein.faa > /dev/null
[2023-03-15 03:51:27,822] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:51:27,823] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg62b710f9-8dd4-444b-a85a-7bddb0f6fa7d/OceanDNA-b13091.fa]
[2023-03-15 03:51:27,843] [INFO] Query marker FASTA was written to OceanDNA-b13091/markers.fasta
[2023-03-15 03:51:27,845] [INFO] Task started: Blastn
[2023-03-15 03:51:27,845] [INFO] Running command: blastn -query OceanDNA-b13091/markers.fasta -db /var/lib/cwl/stge6c704df-f4bf-42be-838d-37019928ec14/dqc_reference/reference_markers.fasta -out OceanDNA-b13091/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:51:28,544] [INFO] Task succeeded: Blastn
[2023-03-15 03:51:28,546] [INFO] Selected 15 target genomes.
[2023-03-15 03:51:28,546] [INFO] Target genome list was writen to OceanDNA-b13091/target_genomes.txt
[2023-03-15 03:51:28,556] [INFO] Task started: fastANI
[2023-03-15 03:51:28,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg62b710f9-8dd4-444b-a85a-7bddb0f6fa7d/OceanDNA-b13091.fa --refList OceanDNA-b13091/target_genomes.txt --output OceanDNA-b13091/fastani_result.tsv --threads 1
[2023-03-15 03:51:41,645] [INFO] Task succeeded: fastANI
[2023-03-15 03:51:41,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6c704df-f4bf-42be-838d-37019928ec14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:51:41,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6c704df-f4bf-42be-838d-37019928ec14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:51:41,651] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:51:41,651] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:51:41,651] [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	85.9311	264	342	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	79.6466	147	342	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.7876	76	342	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.0826	88	342	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.021	68	342	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.0132	69	342	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:51:41,652] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13091/tc_result.tsv
[2023-03-15 03:51:41,653] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:51:41,653] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:51:41,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6c704df-f4bf-42be-838d-37019928ec14/dqc_reference/checkm_data
[2023-03-15 03:51:41,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:51:41,659] [INFO] Task started: CheckM
[2023-03-15 03:51:41,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13091/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13091/checkm_input OceanDNA-b13091/checkm_result
[2023-03-15 03:52:19,424] [INFO] Task succeeded: CheckM
[2023-03-15 03:52:19,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:52:19,439] [INFO] ===== Completeness check finished =====
[2023-03-15 03:52:19,440] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:52:19,440] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13091/markers.fasta)
[2023-03-15 03:52:19,441] [INFO] Task started: Blastn
[2023-03-15 03:52:19,441] [INFO] Running command: blastn -query OceanDNA-b13091/markers.fasta -db /var/lib/cwl/stge6c704df-f4bf-42be-838d-37019928ec14/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13091/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:52:20,674] [INFO] Task succeeded: Blastn
[2023-03-15 03:52:20,677] [INFO] Selected 6 target genomes.
[2023-03-15 03:52:20,677] [INFO] Target genome list was writen to OceanDNA-b13091/target_genomes_gtdb.txt
[2023-03-15 03:52:20,683] [INFO] Task started: fastANI
[2023-03-15 03:52:20,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg62b710f9-8dd4-444b-a85a-7bddb0f6fa7d/OceanDNA-b13091.fa --refList OceanDNA-b13091/target_genomes_gtdb.txt --output OceanDNA-b13091/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:52:24,504] [INFO] Task succeeded: fastANI
[2023-03-15 03:52:24,508] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:52:24,509] [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_002283365.1	s__Rubrivirga marina	85.9311	264	342	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	85.3554	203	342	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	82.3298	233	342	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	80.9392	168	342	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	79.692	148	342	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	78.2069	75	342	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:52:24,509] [INFO] GTDB search result was written to OceanDNA-b13091/result_gtdb.tsv
[2023-03-15 03:52:24,510] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:52:24,512] [INFO] DFAST_QC result json was written to OceanDNA-b13091/dqc_result.json
[2023-03-15 03:52:24,512] [INFO] DFAST_QC completed!
[2023-03-15 03:52:24,513] [INFO] Total running time: 0h1m12s