[2023-03-15 11:09:10,809] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,809] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg32dece38-a82f-4410-990d-f2a2d2b91706/dqc_reference
[2023-03-15 11:09:12,034] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,035] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,035] [INFO] Running command: cat /var/lib/cwl/stg111e8b4a-7c88-4bbb-9419-12bd621e1b17/OceanDNA-b45652.fa | prodigal -d OceanDNA-b45652/cds.fna -a OceanDNA-b45652/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:27,687] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:27,688] [INFO] Task started: HMMsearch
[2023-03-15 11:09:27,688] [INFO] Running command: hmmsearch --tblout OceanDNA-b45652/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32dece38-a82f-4410-990d-f2a2d2b91706/dqc_reference/reference_markers.hmm OceanDNA-b45652/protein.faa > /dev/null
[2023-03-15 11:09:27,937] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:27,937] [INFO] Found 6/6 markers.
[2023-03-15 11:09:27,954] [INFO] Query marker FASTA was written to OceanDNA-b45652/markers.fasta
[2023-03-15 11:09:27,955] [INFO] Task started: Blastn
[2023-03-15 11:09:27,955] [INFO] Running command: blastn -query OceanDNA-b45652/markers.fasta -db /var/lib/cwl/stg32dece38-a82f-4410-990d-f2a2d2b91706/dqc_reference/reference_markers.fasta -out OceanDNA-b45652/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:28,516] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:28,517] [INFO] Selected 17 target genomes.
[2023-03-15 11:09:28,517] [INFO] Target genome list was writen to OceanDNA-b45652/target_genomes.txt
[2023-03-15 11:09:28,527] [INFO] Task started: fastANI
[2023-03-15 11:09:28,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg111e8b4a-7c88-4bbb-9419-12bd621e1b17/OceanDNA-b45652.fa --refList OceanDNA-b45652/target_genomes.txt --output OceanDNA-b45652/fastani_result.tsv --threads 1
[2023-03-15 11:09:37,155] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:37,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32dece38-a82f-4410-990d-f2a2d2b91706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:37,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32dece38-a82f-4410-990d-f2a2d2b91706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:37,156] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:37,156] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:09:37,156] [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 11:09:37,156] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45652/tc_result.tsv
[2023-03-15 11:09:37,156] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:37,156] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:37,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32dece38-a82f-4410-990d-f2a2d2b91706/dqc_reference/checkm_data
[2023-03-15 11:09:37,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:37,164] [INFO] Task started: CheckM
[2023-03-15 11:09:37,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45652/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45652/checkm_input OceanDNA-b45652/checkm_result
[2023-03-15 11:10:20,057] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:20,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:20,059] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:20,060] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:20,060] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45652/markers.fasta)
[2023-03-15 11:10:20,060] [INFO] Task started: Blastn
[2023-03-15 11:10:20,060] [INFO] Running command: blastn -query OceanDNA-b45652/markers.fasta -db /var/lib/cwl/stg32dece38-a82f-4410-990d-f2a2d2b91706/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45652/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:20,974] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:20,975] [INFO] Selected 28 target genomes.
[2023-03-15 11:10:20,975] [INFO] Target genome list was writen to OceanDNA-b45652/target_genomes_gtdb.txt
[2023-03-15 11:10:20,999] [INFO] Task started: fastANI
[2023-03-15 11:10:20,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg111e8b4a-7c88-4bbb-9419-12bd621e1b17/OceanDNA-b45652.fa --refList OceanDNA-b45652/target_genomes_gtdb.txt --output OceanDNA-b45652/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:33,157] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:33,161] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:33,161] [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_902612125.1	s__MB11C04 sp902612125	77.0417	91	652	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689665.1	s__MB11C04 sp002689665	76.784	91	652	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167265.1	s__MB11C04 sp002167265	76.1862	66	652	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:33,161] [INFO] GTDB search result was written to OceanDNA-b45652/result_gtdb.tsv
[2023-03-15 11:10:33,161] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:33,162] [INFO] DFAST_QC result json was written to OceanDNA-b45652/dqc_result.json
[2023-03-15 11:10:33,162] [INFO] DFAST_QC completed!
[2023-03-15 11:10:33,162] [INFO] Total running time: 0h1m22s