[2023-03-17 04:48:54,008] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:54,008] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:54,008] [INFO] DQC Reference Directory: /var/lib/cwl/stg38e175c7-38d8-41de-a58c-1db21a594f42/dqc_reference
[2023-03-17 04:48:55,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,175] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,175] [INFO] Running command: cat /var/lib/cwl/stgb624b609-6e9a-49d1-a568-3120b88ffd19/OceanDNA-b17167.fa | prodigal -d OceanDNA-b17167/cds.fna -a OceanDNA-b17167/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:02,239] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:02,240] [INFO] Task started: HMMsearch
[2023-03-17 04:49:02,240] [INFO] Running command: hmmsearch --tblout OceanDNA-b17167/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38e175c7-38d8-41de-a58c-1db21a594f42/dqc_reference/reference_markers.hmm OceanDNA-b17167/protein.faa > /dev/null
[2023-03-17 04:49:02,410] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:02,411] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb624b609-6e9a-49d1-a568-3120b88ffd19/OceanDNA-b17167.fa]
[2023-03-17 04:49:02,421] [INFO] Query marker FASTA was written to OceanDNA-b17167/markers.fasta
[2023-03-17 04:49:02,422] [INFO] Task started: Blastn
[2023-03-17 04:49:02,422] [INFO] Running command: blastn -query OceanDNA-b17167/markers.fasta -db /var/lib/cwl/stg38e175c7-38d8-41de-a58c-1db21a594f42/dqc_reference/reference_markers.fasta -out OceanDNA-b17167/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:02,929] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:02,929] [INFO] Selected 20 target genomes.
[2023-03-17 04:49:02,930] [INFO] Target genome list was writen to OceanDNA-b17167/target_genomes.txt
[2023-03-17 04:49:02,941] [INFO] Task started: fastANI
[2023-03-17 04:49:02,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgb624b609-6e9a-49d1-a568-3120b88ffd19/OceanDNA-b17167.fa --refList OceanDNA-b17167/target_genomes.txt --output OceanDNA-b17167/fastani_result.tsv --threads 1
[2023-03-17 04:49:09,818] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:09,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38e175c7-38d8-41de-a58c-1db21a594f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:09,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38e175c7-38d8-41de-a58c-1db21a594f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:09,818] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:09,818] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:09,819] [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 04:49:09,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17167/tc_result.tsv
[2023-03-17 04:49:09,819] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:09,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:09,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38e175c7-38d8-41de-a58c-1db21a594f42/dqc_reference/checkm_data
[2023-03-17 04:49:09,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:09,824] [INFO] Task started: CheckM
[2023-03-17 04:49:09,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17167/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17167/checkm_input OceanDNA-b17167/checkm_result
[2023-03-17 04:49:32,681] [INFO] Task succeeded: CheckM
[2023-03-17 04:49:32,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:49:32,683] [INFO] ===== Completeness check finished =====
[2023-03-17 04:49:32,683] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:49:32,683] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17167/markers.fasta)
[2023-03-17 04:49:32,683] [INFO] Task started: Blastn
[2023-03-17 04:49:32,683] [INFO] Running command: blastn -query OceanDNA-b17167/markers.fasta -db /var/lib/cwl/stg38e175c7-38d8-41de-a58c-1db21a594f42/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17167/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:33,365] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:33,365] [INFO] Selected 20 target genomes.
[2023-03-17 04:49:33,366] [INFO] Target genome list was writen to OceanDNA-b17167/target_genomes_gtdb.txt
[2023-03-17 04:49:33,977] [INFO] Task started: fastANI
[2023-03-17 04:49:33,977] [INFO] Running command: fastANI --query /var/lib/cwl/stgb624b609-6e9a-49d1-a568-3120b88ffd19/OceanDNA-b17167.fa --refList OceanDNA-b17167/target_genomes_gtdb.txt --output OceanDNA-b17167/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:49:40,239] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:40,244] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:49:40,244] [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_004195325.1	s__Izemoplasma_B sp004195325	82.471	279	458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__Izemoplasmataceae;g__Izemoplasma_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000755705.1	s__Izemoplasma_B sp000755705	77.6332	107	458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__Izemoplasmataceae;g__Izemoplasma_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000753575.1	s__Izemoplasma_B sp000753575	77.5107	111	458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__Izemoplasmataceae;g__Izemoplasma_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285055.1	s__Izemopslasma_C sp002285055	77.1726	91	458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__Izemoplasmataceae;g__Izemopslasma_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936415.1	s__Izemoplasma_B sp016936415	76.8678	68	458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__Izemoplasmataceae;g__Izemoplasma_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376065.1	s__UBA3566 sp002376065	76.8406	56	458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__Izemoplasmataceae;g__UBA3566	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:49:40,244] [INFO] GTDB search result was written to OceanDNA-b17167/result_gtdb.tsv
[2023-03-17 04:49:40,244] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:49:40,245] [INFO] DFAST_QC result json was written to OceanDNA-b17167/dqc_result.json
[2023-03-17 04:49:40,245] [INFO] DFAST_QC completed!
[2023-03-17 04:49:40,245] [INFO] Total running time: 0h0m46s