[2023-03-16 08:02:40,417] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:02:40,418] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:02:40,418] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb64c897-7741-4139-b991-cce9a972792f/dqc_reference
[2023-03-16 08:02:41,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:02:41,599] [INFO] Task started: Prodigal
[2023-03-16 08:02:41,599] [INFO] Running command: cat /var/lib/cwl/stg95f7ab69-910b-44d6-9cc3-8ab4c074aa5b/OceanDNA-b14740.fa | prodigal -d OceanDNA-b14740/cds.fna -a OceanDNA-b14740/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:02:45,536] [INFO] Task succeeded: Prodigal
[2023-03-16 08:02:45,536] [INFO] Task started: HMMsearch
[2023-03-16 08:02:45,536] [INFO] Running command: hmmsearch --tblout OceanDNA-b14740/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb64c897-7741-4139-b991-cce9a972792f/dqc_reference/reference_markers.hmm OceanDNA-b14740/protein.faa > /dev/null
[2023-03-16 08:02:45,663] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:02:45,663] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg95f7ab69-910b-44d6-9cc3-8ab4c074aa5b/OceanDNA-b14740.fa]
[2023-03-16 08:02:45,677] [INFO] Query marker FASTA was written to OceanDNA-b14740/markers.fasta
[2023-03-16 08:02:45,677] [INFO] Task started: Blastn
[2023-03-16 08:02:45,677] [INFO] Running command: blastn -query OceanDNA-b14740/markers.fasta -db /var/lib/cwl/stgbb64c897-7741-4139-b991-cce9a972792f/dqc_reference/reference_markers.fasta -out OceanDNA-b14740/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:02:46,241] [INFO] Task succeeded: Blastn
[2023-03-16 08:02:46,243] [INFO] Selected 11 target genomes.
[2023-03-16 08:02:46,244] [INFO] Target genome list was writen to OceanDNA-b14740/target_genomes.txt
[2023-03-16 08:02:46,379] [INFO] Task started: fastANI
[2023-03-16 08:02:46,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg95f7ab69-910b-44d6-9cc3-8ab4c074aa5b/OceanDNA-b14740.fa --refList OceanDNA-b14740/target_genomes.txt --output OceanDNA-b14740/fastani_result.tsv --threads 1
[2023-03-16 08:02:50,242] [INFO] Task succeeded: fastANI
[2023-03-16 08:02:50,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb64c897-7741-4139-b991-cce9a972792f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:02:50,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb64c897-7741-4139-b991-cce9a972792f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:02:50,243] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:02:50,243] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:02:50,243] [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
--------------------------------------------------------------------------------
[2023-03-16 08:02:50,245] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14740/tc_result.tsv
[2023-03-16 08:02:50,245] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:02:50,245] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:02:50,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb64c897-7741-4139-b991-cce9a972792f/dqc_reference/checkm_data
[2023-03-16 08:02:50,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:02:50,252] [INFO] Task started: CheckM
[2023-03-16 08:02:50,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14740/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14740/checkm_input OceanDNA-b14740/checkm_result
[2023-03-16 08:03:10,781] [INFO] Task succeeded: CheckM
[2023-03-16 08:03:10,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:03:10,921] [INFO] ===== Completeness check finished =====
[2023-03-16 08:03:10,921] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:03:10,921] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14740/markers.fasta)
[2023-03-16 08:03:10,921] [INFO] Task started: Blastn
[2023-03-16 08:03:10,921] [INFO] Running command: blastn -query OceanDNA-b14740/markers.fasta -db /var/lib/cwl/stgbb64c897-7741-4139-b991-cce9a972792f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14740/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:03:11,524] [INFO] Task succeeded: Blastn
[2023-03-16 08:03:11,556] [INFO] Selected 14 target genomes.
[2023-03-16 08:03:11,556] [INFO] Target genome list was writen to OceanDNA-b14740/target_genomes_gtdb.txt
[2023-03-16 08:03:11,948] [INFO] Task started: fastANI
[2023-03-16 08:03:11,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg95f7ab69-910b-44d6-9cc3-8ab4c074aa5b/OceanDNA-b14740.fa --refList OceanDNA-b14740/target_genomes_gtdb.txt --output OceanDNA-b14740/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:03:15,682] [INFO] Task succeeded: fastANI
[2023-03-16 08:03:15,685] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:03:15,686] [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
GCA_902620405.1	s__GCA-002700125 sp902620405	87.5186	179	254	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727435.1	s__GCA-002700125 sp002727435	85.0686	126	254	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721675.1	s__GCA-002700125 sp002721675	77.0701	60	254	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723375.1	s__GCA-002700125 sp002723375	76.9307	51	254	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	96.02	96.02	0.65	0.65	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:03:15,696] [INFO] GTDB search result was written to OceanDNA-b14740/result_gtdb.tsv
[2023-03-16 08:03:15,716] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:03:15,735] [INFO] DFAST_QC result json was written to OceanDNA-b14740/dqc_result.json
[2023-03-16 08:03:15,736] [INFO] DFAST_QC completed!
[2023-03-16 08:03:15,736] [INFO] Total running time: 0h0m35s