[2023-03-18 07:54:29,581] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:29,581] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:29,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg4eb21bb6-66ad-4267-bf5b-479f701d59e4/dqc_reference
[2023-03-18 07:54:30,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:30,681] [INFO] Task started: Prodigal
[2023-03-18 07:54:30,681] [INFO] Running command: cat /var/lib/cwl/stgdb11135b-13e8-4d33-bc8c-8cce6e94e4c1/OceanDNA-b20494.fa | prodigal -d OceanDNA-b20494/cds.fna -a OceanDNA-b20494/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:36,758] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:36,759] [INFO] Task started: HMMsearch
[2023-03-18 07:54:36,759] [INFO] Running command: hmmsearch --tblout OceanDNA-b20494/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4eb21bb6-66ad-4267-bf5b-479f701d59e4/dqc_reference/reference_markers.hmm OceanDNA-b20494/protein.faa > /dev/null
[2023-03-18 07:54:36,935] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:36,935] [INFO] Found 6/6 markers.
[2023-03-18 07:54:36,951] [INFO] Query marker FASTA was written to OceanDNA-b20494/markers.fasta
[2023-03-18 07:54:36,951] [INFO] Task started: Blastn
[2023-03-18 07:54:36,951] [INFO] Running command: blastn -query OceanDNA-b20494/markers.fasta -db /var/lib/cwl/stg4eb21bb6-66ad-4267-bf5b-479f701d59e4/dqc_reference/reference_markers.fasta -out OceanDNA-b20494/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:37,501] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:37,503] [INFO] Selected 22 target genomes.
[2023-03-18 07:54:37,503] [INFO] Target genome list was writen to OceanDNA-b20494/target_genomes.txt
[2023-03-18 07:54:37,514] [INFO] Task started: fastANI
[2023-03-18 07:54:37,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb11135b-13e8-4d33-bc8c-8cce6e94e4c1/OceanDNA-b20494.fa --refList OceanDNA-b20494/target_genomes.txt --output OceanDNA-b20494/fastani_result.tsv --threads 1
[2023-03-18 07:54:46,116] [INFO] Task succeeded: fastANI
[2023-03-18 07:54:46,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4eb21bb6-66ad-4267-bf5b-479f701d59e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:54:46,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4eb21bb6-66ad-4267-bf5b-479f701d59e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:54:46,117] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:54:46,117] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:54:46,117] [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
--------------------------------------------------------------------------------
[2023-03-18 07:54:46,118] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20494/tc_result.tsv
[2023-03-18 07:54:46,119] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:54:46,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:54:46,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4eb21bb6-66ad-4267-bf5b-479f701d59e4/dqc_reference/checkm_data
[2023-03-18 07:54:46,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:54:46,126] [INFO] Task started: CheckM
[2023-03-18 07:54:46,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20494/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20494/checkm_input OceanDNA-b20494/checkm_result
[2023-03-18 07:55:07,009] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:07,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:55:07,012] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:07,012] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:07,012] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20494/markers.fasta)
[2023-03-18 07:55:07,013] [INFO] Task started: Blastn
[2023-03-18 07:55:07,013] [INFO] Running command: blastn -query OceanDNA-b20494/markers.fasta -db /var/lib/cwl/stg4eb21bb6-66ad-4267-bf5b-479f701d59e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20494/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:07,905] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:07,906] [INFO] Selected 23 target genomes.
[2023-03-18 07:55:07,906] [INFO] Target genome list was writen to OceanDNA-b20494/target_genomes_gtdb.txt
[2023-03-18 07:55:08,010] [INFO] Task started: fastANI
[2023-03-18 07:55:08,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb11135b-13e8-4d33-bc8c-8cce6e94e4c1/OceanDNA-b20494.fa --refList OceanDNA-b20494/target_genomes_gtdb.txt --output OceanDNA-b20494/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:55:14,945] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:14,948] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:55:14,948] [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_002704045.1	s__GCA-002704045 sp002704045	99.1012	306	378	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002704045;g__GCA-002704045	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002703375.1	s__GCA-002704045 sp002703375	90.8957	333	378	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002704045;g__GCA-002704045	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:55:14,948] [INFO] GTDB search result was written to OceanDNA-b20494/result_gtdb.tsv
[2023-03-18 07:55:14,948] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:55:14,948] [INFO] DFAST_QC result json was written to OceanDNA-b20494/dqc_result.json
[2023-03-18 07:55:14,949] [INFO] DFAST_QC completed!
[2023-03-18 07:55:14,949] [INFO] Total running time: 0h0m45s