[2023-03-16 09:23:09,459] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:23:09,459] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:23:09,459] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbb913bd-3965-464e-a5a6-a00fb2c60eca/dqc_reference
[2023-03-16 09:23:11,216] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:23:11,217] [INFO] Task started: Prodigal
[2023-03-16 09:23:11,217] [INFO] Running command: cat /var/lib/cwl/stg905a6620-83a5-4367-918d-f963d7156bd6/OceanDNA-b14627.fa | prodigal -d OceanDNA-b14627/cds.fna -a OceanDNA-b14627/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:23:16,675] [INFO] Task succeeded: Prodigal
[2023-03-16 09:23:16,675] [INFO] Task started: HMMsearch
[2023-03-16 09:23:16,675] [INFO] Running command: hmmsearch --tblout OceanDNA-b14627/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbb913bd-3965-464e-a5a6-a00fb2c60eca/dqc_reference/reference_markers.hmm OceanDNA-b14627/protein.faa > /dev/null
[2023-03-16 09:23:16,798] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:23:16,799] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg905a6620-83a5-4367-918d-f963d7156bd6/OceanDNA-b14627.fa]
[2023-03-16 09:23:16,812] [INFO] Query marker FASTA was written to OceanDNA-b14627/markers.fasta
[2023-03-16 09:23:16,812] [INFO] Task started: Blastn
[2023-03-16 09:23:16,813] [INFO] Running command: blastn -query OceanDNA-b14627/markers.fasta -db /var/lib/cwl/stgfbb913bd-3965-464e-a5a6-a00fb2c60eca/dqc_reference/reference_markers.fasta -out OceanDNA-b14627/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:23:18,390] [INFO] Task succeeded: Blastn
[2023-03-16 09:23:18,392] [INFO] Selected 15 target genomes.
[2023-03-16 09:23:18,392] [INFO] Target genome list was writen to OceanDNA-b14627/target_genomes.txt
[2023-03-16 09:23:18,403] [INFO] Task started: fastANI
[2023-03-16 09:23:18,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg905a6620-83a5-4367-918d-f963d7156bd6/OceanDNA-b14627.fa --refList OceanDNA-b14627/target_genomes.txt --output OceanDNA-b14627/fastani_result.tsv --threads 1
[2023-03-16 09:23:30,670] [INFO] Task succeeded: fastANI
[2023-03-16 09:23:30,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbb913bd-3965-464e-a5a6-a00fb2c60eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:23:30,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbb913bd-3965-464e-a5a6-a00fb2c60eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:23:30,671] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:23:30,671] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:23:30,671] [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 09:23:30,672] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14627/tc_result.tsv
[2023-03-16 09:23:30,673] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:23:30,673] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:23:30,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbb913bd-3965-464e-a5a6-a00fb2c60eca/dqc_reference/checkm_data
[2023-03-16 09:23:30,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:23:30,700] [INFO] Task started: CheckM
[2023-03-16 09:23:30,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14627/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14627/checkm_input OceanDNA-b14627/checkm_result
[2023-03-16 09:23:50,580] [INFO] Task succeeded: CheckM
[2023-03-16 09:23:50,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.45%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 09:23:50,600] [INFO] ===== Completeness check finished =====
[2023-03-16 09:23:50,600] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:23:50,600] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14627/markers.fasta)
[2023-03-16 09:23:50,601] [INFO] Task started: Blastn
[2023-03-16 09:23:50,601] [INFO] Running command: blastn -query OceanDNA-b14627/markers.fasta -db /var/lib/cwl/stgfbb913bd-3965-464e-a5a6-a00fb2c60eca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14627/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:23:51,241] [INFO] Task succeeded: Blastn
[2023-03-16 09:23:51,243] [INFO] Selected 24 target genomes.
[2023-03-16 09:23:51,243] [INFO] Target genome list was writen to OceanDNA-b14627/target_genomes_gtdb.txt
[2023-03-16 09:23:51,298] [INFO] Task started: fastANI
[2023-03-16 09:23:51,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg905a6620-83a5-4367-918d-f963d7156bd6/OceanDNA-b14627.fa --refList OceanDNA-b14627/target_genomes_gtdb.txt --output OceanDNA-b14627/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:24:02,779] [INFO] Task succeeded: fastANI
[2023-03-16 09:24:02,782] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:24:02,783] [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_012959765.1	s__UBA1328 sp012959765	79.9504	155	286	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.88	99.88	0.97	0.97	2	-
GCA_002501045.1	s__UBA1328 sp002501045	77.3783	83	286	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.73	99.73	0.84	0.84	2	-
GCA_018649665.1	s__UBA1328 sp018649665	76.9562	91	286	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673955.1	s__UBA1328 sp018673955	76.8882	88	286	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.55	99.47	0.91	0.89	13	-
--------------------------------------------------------------------------------
[2023-03-16 09:24:02,784] [INFO] GTDB search result was written to OceanDNA-b14627/result_gtdb.tsv
[2023-03-16 09:24:02,784] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:24:02,785] [INFO] DFAST_QC result json was written to OceanDNA-b14627/dqc_result.json
[2023-03-16 09:24:02,785] [INFO] DFAST_QC completed!
[2023-03-16 09:24:02,785] [INFO] Total running time: 0h0m53s