[2023-03-18 09:41:07,187] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,187] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg99c8c940-006f-4b56-8294-c94cea4dc928/dqc_reference
[2023-03-18 09:41:08,290] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,290] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,290] [INFO] Running command: cat /var/lib/cwl/stgda8f3636-8bdd-49bc-a399-9106bf26d5d4/OceanDNA-b14467.fa | prodigal -d OceanDNA-b14467/cds.fna -a OceanDNA-b14467/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:11,132] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:11,133] [INFO] Task started: HMMsearch
[2023-03-18 09:41:11,133] [INFO] Running command: hmmsearch --tblout OceanDNA-b14467/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99c8c940-006f-4b56-8294-c94cea4dc928/dqc_reference/reference_markers.hmm OceanDNA-b14467/protein.faa > /dev/null
[2023-03-18 09:41:11,258] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:11,258] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgda8f3636-8bdd-49bc-a399-9106bf26d5d4/OceanDNA-b14467.fa]
[2023-03-18 09:41:11,266] [INFO] Query marker FASTA was written to OceanDNA-b14467/markers.fasta
[2023-03-18 09:41:11,266] [INFO] Task started: Blastn
[2023-03-18 09:41:11,266] [INFO] Running command: blastn -query OceanDNA-b14467/markers.fasta -db /var/lib/cwl/stg99c8c940-006f-4b56-8294-c94cea4dc928/dqc_reference/reference_markers.fasta -out OceanDNA-b14467/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:11,696] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:11,697] [INFO] Selected 9 target genomes.
[2023-03-18 09:41:11,697] [INFO] Target genome list was writen to OceanDNA-b14467/target_genomes.txt
[2023-03-18 09:41:11,703] [INFO] Task started: fastANI
[2023-03-18 09:41:11,704] [INFO] Running command: fastANI --query /var/lib/cwl/stgda8f3636-8bdd-49bc-a399-9106bf26d5d4/OceanDNA-b14467.fa --refList OceanDNA-b14467/target_genomes.txt --output OceanDNA-b14467/fastani_result.tsv --threads 1
[2023-03-18 09:41:16,217] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:16,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99c8c940-006f-4b56-8294-c94cea4dc928/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:16,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99c8c940-006f-4b56-8294-c94cea4dc928/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:16,218] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:16,218] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:16,218] [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 09:41:16,218] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14467/tc_result.tsv
[2023-03-18 09:41:16,218] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:16,218] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:16,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99c8c940-006f-4b56-8294-c94cea4dc928/dqc_reference/checkm_data
[2023-03-18 09:41:16,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:16,223] [INFO] Task started: CheckM
[2023-03-18 09:41:16,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14467/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14467/checkm_input OceanDNA-b14467/checkm_result
[2023-03-18 09:41:30,146] [INFO] Task succeeded: CheckM
[2023-03-18 09:41:30,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 32.86%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:41:30,148] [INFO] ===== Completeness check finished =====
[2023-03-18 09:41:30,148] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:41:30,148] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14467/markers.fasta)
[2023-03-18 09:41:30,149] [INFO] Task started: Blastn
[2023-03-18 09:41:30,149] [INFO] Running command: blastn -query OceanDNA-b14467/markers.fasta -db /var/lib/cwl/stg99c8c940-006f-4b56-8294-c94cea4dc928/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14467/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:30,570] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:30,571] [INFO] Selected 9 target genomes.
[2023-03-18 09:41:30,571] [INFO] Target genome list was writen to OceanDNA-b14467/target_genomes_gtdb.txt
[2023-03-18 09:41:30,580] [INFO] Task started: fastANI
[2023-03-18 09:41:30,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgda8f3636-8bdd-49bc-a399-9106bf26d5d4/OceanDNA-b14467.fa --refList OceanDNA-b14467/target_genomes_gtdb.txt --output OceanDNA-b14467/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:41:33,357] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:33,361] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:41:33,361] [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_002725925.1	s__GCA-002725925 sp002725925	93.2669	102	128	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687335.1	s__GCA-002725925 sp002687335	84.4734	60	128	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008373165.1	s__GCA-002725925 sp009392785	82.9004	112	128	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	98.70	97.00	0.83	0.72	6	-
GCA_009392215.1	s__GCA-002725925 sp009392215	82.0346	106	128	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:41:33,361] [INFO] GTDB search result was written to OceanDNA-b14467/result_gtdb.tsv
[2023-03-18 09:41:33,361] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:41:33,362] [INFO] DFAST_QC result json was written to OceanDNA-b14467/dqc_result.json
[2023-03-18 09:41:33,362] [INFO] DFAST_QC completed!
[2023-03-18 09:41:33,362] [INFO] Total running time: 0h0m26s