[2023-03-17 07:28:30,365] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:30,365] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:30,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg0de9dc73-9841-4a08-b46f-2c65254b6be4/dqc_reference
[2023-03-17 07:28:31,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:31,524] [INFO] Task started: Prodigal
[2023-03-17 07:28:31,524] [INFO] Running command: cat /var/lib/cwl/stg9b275054-22b6-47bc-8267-b1f6db0ac1c7/OceanDNA-b13197.fa | prodigal -d OceanDNA-b13197/cds.fna -a OceanDNA-b13197/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:55,318] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:55,318] [INFO] Task started: HMMsearch
[2023-03-17 07:28:55,318] [INFO] Running command: hmmsearch --tblout OceanDNA-b13197/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0de9dc73-9841-4a08-b46f-2c65254b6be4/dqc_reference/reference_markers.hmm OceanDNA-b13197/protein.faa > /dev/null
[2023-03-17 07:28:55,523] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:55,524] [INFO] Found 6/6 markers.
[2023-03-17 07:28:55,550] [INFO] Query marker FASTA was written to OceanDNA-b13197/markers.fasta
[2023-03-17 07:28:55,551] [INFO] Task started: Blastn
[2023-03-17 07:28:55,551] [INFO] Running command: blastn -query OceanDNA-b13197/markers.fasta -db /var/lib/cwl/stg0de9dc73-9841-4a08-b46f-2c65254b6be4/dqc_reference/reference_markers.fasta -out OceanDNA-b13197/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:56,068] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:56,069] [INFO] Selected 22 target genomes.
[2023-03-17 07:28:56,069] [INFO] Target genome list was writen to OceanDNA-b13197/target_genomes.txt
[2023-03-17 07:28:56,079] [INFO] Task started: fastANI
[2023-03-17 07:28:56,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b275054-22b6-47bc-8267-b1f6db0ac1c7/OceanDNA-b13197.fa --refList OceanDNA-b13197/target_genomes.txt --output OceanDNA-b13197/fastani_result.tsv --threads 1
[2023-03-17 07:29:08,284] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:08,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0de9dc73-9841-4a08-b46f-2c65254b6be4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:29:08,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0de9dc73-9841-4a08-b46f-2c65254b6be4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:29:08,285] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:29:08,285] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:29:08,285] [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 07:29:08,286] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13197/tc_result.tsv
[2023-03-17 07:29:08,286] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:29:08,286] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:29:08,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0de9dc73-9841-4a08-b46f-2c65254b6be4/dqc_reference/checkm_data
[2023-03-17 07:29:08,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:29:08,302] [INFO] Task started: CheckM
[2023-03-17 07:29:08,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13197/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13197/checkm_input OceanDNA-b13197/checkm_result
[2023-03-17 07:30:07,677] [INFO] Task succeeded: CheckM
[2023-03-17 07:30:07,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:30:07,680] [INFO] ===== Completeness check finished =====
[2023-03-17 07:30:07,680] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:30:07,681] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13197/markers.fasta)
[2023-03-17 07:30:07,681] [INFO] Task started: Blastn
[2023-03-17 07:30:07,681] [INFO] Running command: blastn -query OceanDNA-b13197/markers.fasta -db /var/lib/cwl/stg0de9dc73-9841-4a08-b46f-2c65254b6be4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13197/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:30:08,426] [INFO] Task succeeded: Blastn
[2023-03-17 07:30:08,426] [INFO] Selected 10 target genomes.
[2023-03-17 07:30:08,427] [INFO] Target genome list was writen to OceanDNA-b13197/target_genomes_gtdb.txt
[2023-03-17 07:30:08,544] [INFO] Task started: fastANI
[2023-03-17 07:30:08,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b275054-22b6-47bc-8267-b1f6db0ac1c7/OceanDNA-b13197.fa --refList OceanDNA-b13197/target_genomes_gtdb.txt --output OceanDNA-b13197/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:30:14,811] [INFO] Task succeeded: fastANI
[2023-03-17 07:30:14,816] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:30:14,816] [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_002256935.1	s__UBA2316 sp002256935	82.6965	700	1321	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__UBA2316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345205.1	s__UBA2316 sp002345205	80.8522	600	1321	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__UBA2316	95.0	99.25	99.25	0.87	0.87	2	-
GCA_002344565.1	s__UBA2316 sp002344565	80.6969	528	1321	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__UBA2316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016785955.1	s__UBA2316 sp016785955	78.2625	304	1321	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__UBA2316	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013752535.1	s__Bdellovibrio sp013752535	76.4476	54	1321	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013359135.1	s__UBA2316 sp013359135	76.3041	65	1321	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__UBA2316	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:30:14,817] [INFO] GTDB search result was written to OceanDNA-b13197/result_gtdb.tsv
[2023-03-17 07:30:14,817] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:30:14,817] [INFO] DFAST_QC result json was written to OceanDNA-b13197/dqc_result.json
[2023-03-17 07:30:14,817] [INFO] DFAST_QC completed!
[2023-03-17 07:30:14,817] [INFO] Total running time: 0h1m44s