[2023-03-17 02:31:12,845] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,846] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg68bba47c-f532-42f8-8d58-0b19acb556a7/dqc_reference
[2023-03-17 02:31:14,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,378] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,378] [INFO] Running command: cat /var/lib/cwl/stg41cc5375-249a-41e9-a0b6-ca6cc791d4ff/OceanDNA-b20685.fa | prodigal -d OceanDNA-b20685/cds.fna -a OceanDNA-b20685/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:18,621] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:18,621] [INFO] Task started: HMMsearch
[2023-03-17 02:31:18,621] [INFO] Running command: hmmsearch --tblout OceanDNA-b20685/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68bba47c-f532-42f8-8d58-0b19acb556a7/dqc_reference/reference_markers.hmm OceanDNA-b20685/protein.faa > /dev/null
[2023-03-17 02:31:18,768] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:18,769] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg41cc5375-249a-41e9-a0b6-ca6cc791d4ff/OceanDNA-b20685.fa]
[2023-03-17 02:31:18,778] [INFO] Query marker FASTA was written to OceanDNA-b20685/markers.fasta
[2023-03-17 02:31:18,778] [INFO] Task started: Blastn
[2023-03-17 02:31:18,778] [INFO] Running command: blastn -query OceanDNA-b20685/markers.fasta -db /var/lib/cwl/stg68bba47c-f532-42f8-8d58-0b19acb556a7/dqc_reference/reference_markers.fasta -out OceanDNA-b20685/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:19,265] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:19,266] [INFO] Selected 10 target genomes.
[2023-03-17 02:31:19,266] [INFO] Target genome list was writen to OceanDNA-b20685/target_genomes.txt
[2023-03-17 02:31:19,272] [INFO] Task started: fastANI
[2023-03-17 02:31:19,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg41cc5375-249a-41e9-a0b6-ca6cc791d4ff/OceanDNA-b20685.fa --refList OceanDNA-b20685/target_genomes.txt --output OceanDNA-b20685/fastani_result.tsv --threads 1
[2023-03-17 02:31:24,569] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:24,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68bba47c-f532-42f8-8d58-0b19acb556a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:24,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68bba47c-f532-42f8-8d58-0b19acb556a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:24,570] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:24,570] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:31:24,570] [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 02:31:24,570] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20685/tc_result.tsv
[2023-03-17 02:31:24,570] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:24,570] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:24,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68bba47c-f532-42f8-8d58-0b19acb556a7/dqc_reference/checkm_data
[2023-03-17 02:31:24,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:24,577] [INFO] Task started: CheckM
[2023-03-17 02:31:24,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20685/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20685/checkm_input OceanDNA-b20685/checkm_result
[2023-03-17 02:31:41,349] [INFO] Task succeeded: CheckM
[2023-03-17 02:31:41,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:31:41,351] [INFO] ===== Completeness check finished =====
[2023-03-17 02:31:41,351] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:31:41,351] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20685/markers.fasta)
[2023-03-17 02:31:41,351] [INFO] Task started: Blastn
[2023-03-17 02:31:41,351] [INFO] Running command: blastn -query OceanDNA-b20685/markers.fasta -db /var/lib/cwl/stg68bba47c-f532-42f8-8d58-0b19acb556a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20685/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:42,010] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:42,011] [INFO] Selected 22 target genomes.
[2023-03-17 02:31:42,011] [INFO] Target genome list was writen to OceanDNA-b20685/target_genomes_gtdb.txt
[2023-03-17 02:31:42,979] [INFO] Task started: fastANI
[2023-03-17 02:31:42,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg41cc5375-249a-41e9-a0b6-ca6cc791d4ff/OceanDNA-b20685.fa --refList OceanDNA-b20685/target_genomes_gtdb.txt --output OceanDNA-b20685/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:31:49,705] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:49,708] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:31:49,708] [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_002731795.1	s__TMED161 sp002731795	76.5309	58	265	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	98.59	98.59	0.77	0.77	2	-
GCA_002703645.1	s__TMED161 sp002703645	76.1725	61	265	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:31:49,708] [INFO] GTDB search result was written to OceanDNA-b20685/result_gtdb.tsv
[2023-03-17 02:31:49,708] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:31:49,709] [INFO] DFAST_QC result json was written to OceanDNA-b20685/dqc_result.json
[2023-03-17 02:31:49,709] [INFO] DFAST_QC completed!
[2023-03-17 02:31:49,709] [INFO] Total running time: 0h0m37s