[2023-03-18 20:13:32,794] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,794] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg725b0b8a-5417-4e09-904e-5ecaa5e1ffd1/dqc_reference
[2023-03-18 20:13:34,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:34,580] [INFO] Task started: Prodigal
[2023-03-18 20:13:34,580] [INFO] Running command: cat /var/lib/cwl/stgae112449-1b67-461b-8ab4-a80f83c13e4c/OceanDNA-b13084.fa | prodigal -d OceanDNA-b13084/cds.fna -a OceanDNA-b13084/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:52,435] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:52,436] [INFO] Task started: HMMsearch
[2023-03-18 20:13:52,436] [INFO] Running command: hmmsearch --tblout OceanDNA-b13084/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg725b0b8a-5417-4e09-904e-5ecaa5e1ffd1/dqc_reference/reference_markers.hmm OceanDNA-b13084/protein.faa > /dev/null
[2023-03-18 20:13:52,579] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:52,580] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgae112449-1b67-461b-8ab4-a80f83c13e4c/OceanDNA-b13084.fa]
[2023-03-18 20:13:52,599] [INFO] Query marker FASTA was written to OceanDNA-b13084/markers.fasta
[2023-03-18 20:13:52,599] [INFO] Task started: Blastn
[2023-03-18 20:13:52,599] [INFO] Running command: blastn -query OceanDNA-b13084/markers.fasta -db /var/lib/cwl/stg725b0b8a-5417-4e09-904e-5ecaa5e1ffd1/dqc_reference/reference_markers.fasta -out OceanDNA-b13084/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:53,110] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:53,111] [INFO] Selected 9 target genomes.
[2023-03-18 20:13:53,111] [INFO] Target genome list was writen to OceanDNA-b13084/target_genomes.txt
[2023-03-18 20:13:53,117] [INFO] Task started: fastANI
[2023-03-18 20:13:53,117] [INFO] Running command: fastANI --query /var/lib/cwl/stgae112449-1b67-461b-8ab4-a80f83c13e4c/OceanDNA-b13084.fa --refList OceanDNA-b13084/target_genomes.txt --output OceanDNA-b13084/fastani_result.tsv --threads 1
[2023-03-18 20:13:59,433] [INFO] Task succeeded: fastANI
[2023-03-18 20:13:59,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg725b0b8a-5417-4e09-904e-5ecaa5e1ffd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:13:59,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg725b0b8a-5417-4e09-904e-5ecaa5e1ffd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:13:59,437] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:13:59,437] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:13:59,437] [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	80.6792	523	718	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	75.6568	91	718	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	74.651	69	718	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:13:59,437] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13084/tc_result.tsv
[2023-03-18 20:13:59,437] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:13:59,437] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:13:59,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg725b0b8a-5417-4e09-904e-5ecaa5e1ffd1/dqc_reference/checkm_data
[2023-03-18 20:13:59,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:13:59,442] [INFO] Task started: CheckM
[2023-03-18 20:13:59,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13084/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13084/checkm_input OceanDNA-b13084/checkm_result
[2023-03-18 20:14:44,180] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:44,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:44,182] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:44,183] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:44,183] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13084/markers.fasta)
[2023-03-18 20:14:44,183] [INFO] Task started: Blastn
[2023-03-18 20:14:44,183] [INFO] Running command: blastn -query OceanDNA-b13084/markers.fasta -db /var/lib/cwl/stg725b0b8a-5417-4e09-904e-5ecaa5e1ffd1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13084/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:44,879] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:44,880] [INFO] Selected 8 target genomes.
[2023-03-18 20:14:44,880] [INFO] Target genome list was writen to OceanDNA-b13084/target_genomes_gtdb.txt
[2023-03-18 20:14:45,090] [INFO] Task started: fastANI
[2023-03-18 20:14:45,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgae112449-1b67-461b-8ab4-a80f83c13e4c/OceanDNA-b13084.fa --refList OceanDNA-b13084/target_genomes_gtdb.txt --output OceanDNA-b13084/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:14:50,823] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:50,828] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:14:50,828] [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	80.6702	523	718	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	80.1034	371	718	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	79.2362	460	718	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	77.4507	257	718	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	77.2372	256	718	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	76.5237	151	718	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:14:50,828] [INFO] GTDB search result was written to OceanDNA-b13084/result_gtdb.tsv
[2023-03-18 20:14:50,828] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:14:50,829] [INFO] DFAST_QC result json was written to OceanDNA-b13084/dqc_result.json
[2023-03-18 20:14:50,829] [INFO] DFAST_QC completed!
[2023-03-18 20:14:50,829] [INFO] Total running time: 0h1m18s