[2023-03-18 01:16:48,380] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:16:48,380] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:16:48,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e2dab10-42b8-4cb0-8df1-a00613b08317/dqc_reference
[2023-03-18 01:16:49,483] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:16:49,484] [INFO] Task started: Prodigal
[2023-03-18 01:16:49,484] [INFO] Running command: cat /var/lib/cwl/stg1f5fc153-c7f1-4387-90ce-6a8c3a0c6eb9/OceanDNA-b32460.fa | prodigal -d OceanDNA-b32460/cds.fna -a OceanDNA-b32460/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:16:56,084] [INFO] Task succeeded: Prodigal
[2023-03-18 01:16:56,084] [INFO] Task started: HMMsearch
[2023-03-18 01:16:56,084] [INFO] Running command: hmmsearch --tblout OceanDNA-b32460/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e2dab10-42b8-4cb0-8df1-a00613b08317/dqc_reference/reference_markers.hmm OceanDNA-b32460/protein.faa > /dev/null
[2023-03-18 01:16:56,242] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:16:56,242] [INFO] Found 6/6 markers.
[2023-03-18 01:16:56,253] [INFO] Query marker FASTA was written to OceanDNA-b32460/markers.fasta
[2023-03-18 01:16:56,255] [INFO] Task started: Blastn
[2023-03-18 01:16:56,255] [INFO] Running command: blastn -query OceanDNA-b32460/markers.fasta -db /var/lib/cwl/stg7e2dab10-42b8-4cb0-8df1-a00613b08317/dqc_reference/reference_markers.fasta -out OceanDNA-b32460/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:16:56,848] [INFO] Task succeeded: Blastn
[2023-03-18 01:16:56,849] [INFO] Selected 21 target genomes.
[2023-03-18 01:16:56,849] [INFO] Target genome list was writen to OceanDNA-b32460/target_genomes.txt
[2023-03-18 01:16:56,858] [INFO] Task started: fastANI
[2023-03-18 01:16:56,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f5fc153-c7f1-4387-90ce-6a8c3a0c6eb9/OceanDNA-b32460.fa --refList OceanDNA-b32460/target_genomes.txt --output OceanDNA-b32460/fastani_result.tsv --threads 1
[2023-03-18 01:17:03,934] [INFO] Task succeeded: fastANI
[2023-03-18 01:17:03,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e2dab10-42b8-4cb0-8df1-a00613b08317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:17:03,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e2dab10-42b8-4cb0-8df1-a00613b08317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:17:03,935] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:17:03,935] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:17:03,935] [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 01:17:03,935] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32460/tc_result.tsv
[2023-03-18 01:17:03,935] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:17:03,935] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:17:03,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e2dab10-42b8-4cb0-8df1-a00613b08317/dqc_reference/checkm_data
[2023-03-18 01:17:03,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:17:03,941] [INFO] Task started: CheckM
[2023-03-18 01:17:03,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32460/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32460/checkm_input OceanDNA-b32460/checkm_result
[2023-03-18 01:17:25,516] [INFO] Task succeeded: CheckM
[2023-03-18 01:17:25,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:17:25,519] [INFO] ===== Completeness check finished =====
[2023-03-18 01:17:25,519] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:17:25,519] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32460/markers.fasta)
[2023-03-18 01:17:25,520] [INFO] Task started: Blastn
[2023-03-18 01:17:25,520] [INFO] Running command: blastn -query OceanDNA-b32460/markers.fasta -db /var/lib/cwl/stg7e2dab10-42b8-4cb0-8df1-a00613b08317/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32460/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:17:26,520] [INFO] Task succeeded: Blastn
[2023-03-18 01:17:26,520] [INFO] Selected 15 target genomes.
[2023-03-18 01:17:26,521] [INFO] Target genome list was writen to OceanDNA-b32460/target_genomes_gtdb.txt
[2023-03-18 01:17:26,536] [INFO] Task started: fastANI
[2023-03-18 01:17:26,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f5fc153-c7f1-4387-90ce-6a8c3a0c6eb9/OceanDNA-b32460.fa --refList OceanDNA-b32460/target_genomes_gtdb.txt --output OceanDNA-b32460/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:17:30,114] [INFO] Task succeeded: fastANI
[2023-03-18 01:17:30,118] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:17:30,118] [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_002937655.1	s__TMED109 sp002937655	99.8964	417	461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	99.81	99.81	0.91	0.91	2	conclusive
GCA_002720535.1	s__TMED109 sp002720535	81.0651	330	461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	95.89	95.27	0.82	0.81	3	-
GCA_002171375.1	s__TMED109 sp002171375	80.5084	253	461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	98.96	97.53	0.84	0.73	4	-
GCA_002684605.1	s__TMED109 sp002684605	77.6182	182	461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660425.1	s__TMED109 sp015660425	77.6182	114	461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715265.1	s__GCA-002727615 sp002715265	76.7774	135	461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__GCA-002727615	95.0	98.23	98.23	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:17:30,119] [INFO] GTDB search result was written to OceanDNA-b32460/result_gtdb.tsv
[2023-03-18 01:17:30,119] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:17:30,119] [INFO] DFAST_QC result json was written to OceanDNA-b32460/dqc_result.json
[2023-03-18 01:17:30,120] [INFO] DFAST_QC completed!
[2023-03-18 01:17:30,120] [INFO] Total running time: 0h0m42s