[2023-03-17 07:01:49,604] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,604] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg40b8a291-73ba-40e6-a66d-2b4d691827ea/dqc_reference
[2023-03-17 07:01:51,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,528] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,528] [INFO] Running command: cat /var/lib/cwl/stg2319f7e9-36b7-42cd-8055-b236c3b67378/OceanDNA-b17082.fa | prodigal -d OceanDNA-b17082/cds.fna -a OceanDNA-b17082/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:05,809] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:05,810] [INFO] Task started: HMMsearch
[2023-03-17 07:02:05,810] [INFO] Running command: hmmsearch --tblout OceanDNA-b17082/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40b8a291-73ba-40e6-a66d-2b4d691827ea/dqc_reference/reference_markers.hmm OceanDNA-b17082/protein.faa > /dev/null
[2023-03-17 07:02:06,029] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:06,029] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2319f7e9-36b7-42cd-8055-b236c3b67378/OceanDNA-b17082.fa]
[2023-03-17 07:02:06,055] [INFO] Query marker FASTA was written to OceanDNA-b17082/markers.fasta
[2023-03-17 07:02:06,056] [INFO] Task started: Blastn
[2023-03-17 07:02:06,056] [INFO] Running command: blastn -query OceanDNA-b17082/markers.fasta -db /var/lib/cwl/stg40b8a291-73ba-40e6-a66d-2b4d691827ea/dqc_reference/reference_markers.fasta -out OceanDNA-b17082/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:06,637] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:06,637] [INFO] Selected 6 target genomes.
[2023-03-17 07:02:06,638] [INFO] Target genome list was writen to OceanDNA-b17082/target_genomes.txt
[2023-03-17 07:02:06,642] [INFO] Task started: fastANI
[2023-03-17 07:02:06,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg2319f7e9-36b7-42cd-8055-b236c3b67378/OceanDNA-b17082.fa --refList OceanDNA-b17082/target_genomes.txt --output OceanDNA-b17082/fastani_result.tsv --threads 1
[2023-03-17 07:02:10,406] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:10,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40b8a291-73ba-40e6-a66d-2b4d691827ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:10,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40b8a291-73ba-40e6-a66d-2b4d691827ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:10,407] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:10,407] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:02:10,407] [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
--------------------------------------------------------------------------------
[2023-03-17 07:02:10,407] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17082/tc_result.tsv
[2023-03-17 07:02:10,407] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:10,407] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:10,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40b8a291-73ba-40e6-a66d-2b4d691827ea/dqc_reference/checkm_data
[2023-03-17 07:02:10,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:10,415] [INFO] Task started: CheckM
[2023-03-17 07:02:10,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17082/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17082/checkm_input OceanDNA-b17082/checkm_result
[2023-03-17 07:02:50,075] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:50,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:50,079] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:50,079] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:50,079] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17082/markers.fasta)
[2023-03-17 07:02:50,079] [INFO] Task started: Blastn
[2023-03-17 07:02:50,079] [INFO] Running command: blastn -query OceanDNA-b17082/markers.fasta -db /var/lib/cwl/stg40b8a291-73ba-40e6-a66d-2b4d691827ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17082/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:51,047] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:51,048] [INFO] Selected 19 target genomes.
[2023-03-17 07:02:51,048] [INFO] Target genome list was writen to OceanDNA-b17082/target_genomes_gtdb.txt
[2023-03-17 07:02:51,626] [INFO] Task started: fastANI
[2023-03-17 07:02:51,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg2319f7e9-36b7-42cd-8055-b236c3b67378/OceanDNA-b17082.fa --refList OceanDNA-b17082/target_genomes_gtdb.txt --output OceanDNA-b17082/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:03:03,690] [INFO] Task succeeded: fastANI
[2023-03-17 07:03:03,693] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:03:03,693] [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_016844935.1	s__NaphS2 sp016844935	84.7394	542	689	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__NaphS2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000179315.1	s__NaphS2 sp000179315	78.6923	259	689	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__NaphS2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:03:03,693] [INFO] GTDB search result was written to OceanDNA-b17082/result_gtdb.tsv
[2023-03-17 07:03:03,694] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:03:03,694] [INFO] DFAST_QC result json was written to OceanDNA-b17082/dqc_result.json
[2023-03-17 07:03:03,694] [INFO] DFAST_QC completed!
[2023-03-17 07:03:03,694] [INFO] Total running time: 0h1m14s