[2023-03-15 03:49:35,832] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:49:35,832] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:49:35,832] [INFO] DQC Reference Directory: /var/lib/cwl/stgb111292f-5fac-48e6-ae73-45e5dadf2f91/dqc_reference
[2023-03-15 03:49:36,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:49:36,937] [INFO] Task started: Prodigal
[2023-03-15 03:49:36,938] [INFO] Running command: cat /var/lib/cwl/stgf29b1741-ee56-4601-a3ca-39e937705d25/OceanDNA-a4.fa | prodigal -d OceanDNA-a4/cds.fna -a OceanDNA-a4/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:49:41,495] [INFO] Task succeeded: Prodigal
[2023-03-15 03:49:41,495] [INFO] Task started: HMMsearch
[2023-03-15 03:49:41,495] [INFO] Running command: hmmsearch --tblout OceanDNA-a4/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb111292f-5fac-48e6-ae73-45e5dadf2f91/dqc_reference/reference_markers.hmm OceanDNA-a4/protein.faa > /dev/null
[2023-03-15 03:49:41,644] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:49:41,644] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf29b1741-ee56-4601-a3ca-39e937705d25/OceanDNA-a4.fa]
[2023-03-15 03:49:41,654] [INFO] Query marker FASTA was written to OceanDNA-a4/markers.fasta
[2023-03-15 03:49:41,655] [INFO] Task started: Blastn
[2023-03-15 03:49:41,655] [INFO] Running command: blastn -query OceanDNA-a4/markers.fasta -db /var/lib/cwl/stgb111292f-5fac-48e6-ae73-45e5dadf2f91/dqc_reference/reference_markers.fasta -out OceanDNA-a4/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:49:42,133] [INFO] Task succeeded: Blastn
[2023-03-15 03:49:42,134] [INFO] Selected 5 target genomes.
[2023-03-15 03:49:42,134] [INFO] Target genome list was writen to OceanDNA-a4/target_genomes.txt
[2023-03-15 03:49:42,138] [INFO] Task started: fastANI
[2023-03-15 03:49:42,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgf29b1741-ee56-4601-a3ca-39e937705d25/OceanDNA-a4.fa --refList OceanDNA-a4/target_genomes.txt --output OceanDNA-a4/fastani_result.tsv --threads 1
[2023-03-15 03:49:42,975] [INFO] Task succeeded: fastANI
[2023-03-15 03:49:42,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb111292f-5fac-48e6-ae73-45e5dadf2f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:49:42,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb111292f-5fac-48e6-ae73-45e5dadf2f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:49:42,976] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:49:42,976] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:49:42,976] [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
--------------------------------------------------------------------------------
[2023-03-15 03:49:42,976] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4/tc_result.tsv
[2023-03-15 03:49:42,976] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:49:42,977] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:49:42,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb111292f-5fac-48e6-ae73-45e5dadf2f91/dqc_reference/checkm_data
[2023-03-15 03:49:42,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:49:42,982] [INFO] Task started: CheckM
[2023-03-15 03:49:42,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4/checkm_input OceanDNA-a4/checkm_result
[2023-03-15 03:50:00,811] [INFO] Task succeeded: CheckM
[2023-03-15 03:50:00,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.01%
Contamintation: 1.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 03:50:00,814] [INFO] ===== Completeness check finished =====
[2023-03-15 03:50:00,814] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:50:00,815] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4/markers.fasta)
[2023-03-15 03:50:00,816] [INFO] Task started: Blastn
[2023-03-15 03:50:00,816] [INFO] Running command: blastn -query OceanDNA-a4/markers.fasta -db /var/lib/cwl/stgb111292f-5fac-48e6-ae73-45e5dadf2f91/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:50:01,394] [INFO] Task succeeded: Blastn
[2023-03-15 03:50:01,396] [INFO] Selected 7 target genomes.
[2023-03-15 03:50:01,396] [INFO] Target genome list was writen to OceanDNA-a4/target_genomes_gtdb.txt
[2023-03-15 03:50:01,404] [INFO] Task started: fastANI
[2023-03-15 03:50:01,404] [INFO] Running command: fastANI --query /var/lib/cwl/stgf29b1741-ee56-4601-a3ca-39e937705d25/OceanDNA-a4.fa --refList OceanDNA-a4/target_genomes_gtdb.txt --output OceanDNA-a4/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:50:03,083] [INFO] Task succeeded: fastANI
[2023-03-15 03:50:03,085] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:50:03,085] [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_002728275.1	s__Kariarchaeum pelagius	99.1148	260	280	d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__Kariarchaeaceae;g__Kariarchaeum	95.0	96.77	96.55	0.77	0.68	4	conclusive
--------------------------------------------------------------------------------
[2023-03-15 03:50:03,086] [INFO] GTDB search result was written to OceanDNA-a4/result_gtdb.tsv
[2023-03-15 03:50:03,086] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:50:03,087] [INFO] DFAST_QC result json was written to OceanDNA-a4/dqc_result.json
[2023-03-15 03:50:03,087] [INFO] DFAST_QC completed!
[2023-03-15 03:50:03,087] [INFO] Total running time: 0h0m27s