[2023-03-14 12:44:46,926] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:44:46,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:44:46,926] [INFO] DQC Reference Directory: /var/lib/cwl/stgb71f6fd5-c397-48ad-951f-a0cb2b6dcccf/dqc_reference
[2023-03-14 12:44:48,020] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:44:48,021] [INFO] Task started: Prodigal
[2023-03-14 12:44:48,021] [INFO] Running command: cat /var/lib/cwl/stgafe380e0-b4b1-4296-ac4d-1324ebe6bebd/OceanDNA-b45557.fa | prodigal -d OceanDNA-b45557/cds.fna -a OceanDNA-b45557/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:45:02,058] [INFO] Task succeeded: Prodigal
[2023-03-14 12:45:02,058] [INFO] Task started: HMMsearch
[2023-03-14 12:45:02,058] [INFO] Running command: hmmsearch --tblout OceanDNA-b45557/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb71f6fd5-c397-48ad-951f-a0cb2b6dcccf/dqc_reference/reference_markers.hmm OceanDNA-b45557/protein.faa > /dev/null
[2023-03-14 12:45:02,305] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:45:02,306] [INFO] Found 6/6 markers.
[2023-03-14 12:45:02,321] [INFO] Query marker FASTA was written to OceanDNA-b45557/markers.fasta
[2023-03-14 12:45:02,332] [INFO] Task started: Blastn
[2023-03-14 12:45:02,332] [INFO] Running command: blastn -query OceanDNA-b45557/markers.fasta -db /var/lib/cwl/stgb71f6fd5-c397-48ad-951f-a0cb2b6dcccf/dqc_reference/reference_markers.fasta -out OceanDNA-b45557/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:45:02,919] [INFO] Task succeeded: Blastn
[2023-03-14 12:45:02,920] [INFO] Selected 11 target genomes.
[2023-03-14 12:45:02,920] [INFO] Target genome list was writen to OceanDNA-b45557/target_genomes.txt
[2023-03-14 12:45:02,927] [INFO] Task started: fastANI
[2023-03-14 12:45:02,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe380e0-b4b1-4296-ac4d-1324ebe6bebd/OceanDNA-b45557.fa --refList OceanDNA-b45557/target_genomes.txt --output OceanDNA-b45557/fastani_result.tsv --threads 1
[2023-03-14 12:45:11,194] [INFO] Task succeeded: fastANI
[2023-03-14 12:45:11,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb71f6fd5-c397-48ad-951f-a0cb2b6dcccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:45:11,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb71f6fd5-c397-48ad-951f-a0cb2b6dcccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:45:11,195] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:45:11,195] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:45:11,195] [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
--------------------------------------------------------------------------------
[2023-03-14 12:45:11,195] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45557/tc_result.tsv
[2023-03-14 12:45:11,196] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:45:11,197] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:45:11,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb71f6fd5-c397-48ad-951f-a0cb2b6dcccf/dqc_reference/checkm_data
[2023-03-14 12:45:11,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:45:11,204] [INFO] Task started: CheckM
[2023-03-14 12:45:11,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45557/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45557/checkm_input OceanDNA-b45557/checkm_result
[2023-03-14 12:46:01,410] [INFO] Task succeeded: CheckM
[2023-03-14 12:46:01,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 7.59%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:46:01,415] [INFO] ===== Completeness check finished =====
[2023-03-14 12:46:01,415] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:46:01,415] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45557/markers.fasta)
[2023-03-14 12:46:01,415] [INFO] Task started: Blastn
[2023-03-14 12:46:01,416] [INFO] Running command: blastn -query OceanDNA-b45557/markers.fasta -db /var/lib/cwl/stgb71f6fd5-c397-48ad-951f-a0cb2b6dcccf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45557/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:46:02,341] [INFO] Task succeeded: Blastn
[2023-03-14 12:46:02,343] [INFO] Selected 23 target genomes.
[2023-03-14 12:46:02,343] [INFO] Target genome list was writen to OceanDNA-b45557/target_genomes_gtdb.txt
[2023-03-14 12:46:02,367] [INFO] Task started: fastANI
[2023-03-14 12:46:02,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe380e0-b4b1-4296-ac4d-1324ebe6bebd/OceanDNA-b45557.fa --refList OceanDNA-b45557/target_genomes_gtdb.txt --output OceanDNA-b45557/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:46:11,941] [INFO] Task succeeded: fastANI
[2023-03-14 12:46:11,944] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:46:11,944] [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_900299365.1	s__MB11C04 sp900299365	98.5139	390	533	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002686835.1	s__MB11C04 sp002686835	79.8294	200	533	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.34	99.34	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:46:11,944] [INFO] GTDB search result was written to OceanDNA-b45557/result_gtdb.tsv
[2023-03-14 12:46:11,945] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:46:11,945] [INFO] DFAST_QC result json was written to OceanDNA-b45557/dqc_result.json
[2023-03-14 12:46:11,946] [INFO] DFAST_QC completed!
[2023-03-14 12:46:11,946] [INFO] Total running time: 0h1m25s