[2023-03-17 03:33:08,353] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:33:08,353] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:33:08,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg29f13bcc-4757-48f9-89a8-c48faa4359dc/dqc_reference
[2023-03-17 03:33:09,443] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:33:09,444] [INFO] Task started: Prodigal
[2023-03-17 03:33:09,444] [INFO] Running command: cat /var/lib/cwl/stg02fc2d3a-cd06-43b6-b6fc-d1dbf05830f9/OceanDNA-b41614.fa | prodigal -d OceanDNA-b41614/cds.fna -a OceanDNA-b41614/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:33:19,432] [INFO] Task succeeded: Prodigal
[2023-03-17 03:33:19,433] [INFO] Task started: HMMsearch
[2023-03-17 03:33:19,433] [INFO] Running command: hmmsearch --tblout OceanDNA-b41614/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29f13bcc-4757-48f9-89a8-c48faa4359dc/dqc_reference/reference_markers.hmm OceanDNA-b41614/protein.faa > /dev/null
[2023-03-17 03:33:19,605] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:33:19,606] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg02fc2d3a-cd06-43b6-b6fc-d1dbf05830f9/OceanDNA-b41614.fa]
[2023-03-17 03:33:19,620] [INFO] Query marker FASTA was written to OceanDNA-b41614/markers.fasta
[2023-03-17 03:33:19,620] [INFO] Task started: Blastn
[2023-03-17 03:33:19,620] [INFO] Running command: blastn -query OceanDNA-b41614/markers.fasta -db /var/lib/cwl/stg29f13bcc-4757-48f9-89a8-c48faa4359dc/dqc_reference/reference_markers.fasta -out OceanDNA-b41614/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:33:20,156] [INFO] Task succeeded: Blastn
[2023-03-17 03:33:20,157] [INFO] Selected 35 target genomes.
[2023-03-17 03:33:20,157] [INFO] Target genome list was writen to OceanDNA-b41614/target_genomes.txt
[2023-03-17 03:33:20,176] [INFO] Task started: fastANI
[2023-03-17 03:33:20,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg02fc2d3a-cd06-43b6-b6fc-d1dbf05830f9/OceanDNA-b41614.fa --refList OceanDNA-b41614/target_genomes.txt --output OceanDNA-b41614/fastani_result.tsv --threads 1
[2023-03-17 03:33:37,461] [INFO] Task succeeded: fastANI
[2023-03-17 03:33:37,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29f13bcc-4757-48f9-89a8-c48faa4359dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:33:37,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29f13bcc-4757-48f9-89a8-c48faa4359dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:33:37,462] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:33:37,462] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:33:37,462] [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 03:33:37,462] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41614/tc_result.tsv
[2023-03-17 03:33:37,462] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:33:37,462] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:33:37,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29f13bcc-4757-48f9-89a8-c48faa4359dc/dqc_reference/checkm_data
[2023-03-17 03:33:37,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:33:37,469] [INFO] Task started: CheckM
[2023-03-17 03:33:37,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41614/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41614/checkm_input OceanDNA-b41614/checkm_result
[2023-03-17 03:34:06,627] [INFO] Task succeeded: CheckM
[2023-03-17 03:34:06,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.98%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 03:34:06,629] [INFO] ===== Completeness check finished =====
[2023-03-17 03:34:06,630] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:34:06,630] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41614/markers.fasta)
[2023-03-17 03:34:06,631] [INFO] Task started: Blastn
[2023-03-17 03:34:06,631] [INFO] Running command: blastn -query OceanDNA-b41614/markers.fasta -db /var/lib/cwl/stg29f13bcc-4757-48f9-89a8-c48faa4359dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41614/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:34:07,338] [INFO] Task succeeded: Blastn
[2023-03-17 03:34:07,339] [INFO] Selected 18 target genomes.
[2023-03-17 03:34:07,339] [INFO] Target genome list was writen to OceanDNA-b41614/target_genomes_gtdb.txt
[2023-03-17 03:34:07,413] [INFO] Task started: fastANI
[2023-03-17 03:34:07,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg02fc2d3a-cd06-43b6-b6fc-d1dbf05830f9/OceanDNA-b41614.fa --refList OceanDNA-b41614/target_genomes_gtdb.txt --output OceanDNA-b41614/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:34:15,112] [INFO] Task succeeded: fastANI
[2023-03-17 03:34:15,115] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:34:15,115] [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_003492055.1	s__UBA7434 sp003492055	87.7168	281	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	98.70	98.70	0.91	0.91	2	-
GCA_018668095.1	s__UBA7434 sp018668095	86.3327	417	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	98.20	98.20	0.79	0.79	2	-
GCA_905480475.1	s__UBA7434 sp905480475	77.6791	125	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339085.1	s__UBA7434 sp002339085	76.1984	55	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.78	99.78	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-17 03:34:15,115] [INFO] GTDB search result was written to OceanDNA-b41614/result_gtdb.tsv
[2023-03-17 03:34:15,116] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:34:15,116] [INFO] DFAST_QC result json was written to OceanDNA-b41614/dqc_result.json
[2023-03-17 03:34:15,116] [INFO] DFAST_QC completed!
[2023-03-17 03:34:15,116] [INFO] Total running time: 0h1m7s