[2023-03-18 10:12:10,176] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:12:10,177] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:12:10,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ab802c2-6d79-4691-9210-f468dedd2f20/dqc_reference
[2023-03-18 10:12:11,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:12:11,359] [INFO] Task started: Prodigal
[2023-03-18 10:12:11,359] [INFO] Running command: cat /var/lib/cwl/stgb11bcd03-744d-4af2-b1d2-8c68939bb9fc/OceanDNA-b35375.fa | prodigal -d OceanDNA-b35375/cds.fna -a OceanDNA-b35375/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:12:21,481] [INFO] Task succeeded: Prodigal
[2023-03-18 10:12:21,481] [INFO] Task started: HMMsearch
[2023-03-18 10:12:21,481] [INFO] Running command: hmmsearch --tblout OceanDNA-b35375/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ab802c2-6d79-4691-9210-f468dedd2f20/dqc_reference/reference_markers.hmm OceanDNA-b35375/protein.faa > /dev/null
[2023-03-18 10:12:21,620] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:12:21,621] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb11bcd03-744d-4af2-b1d2-8c68939bb9fc/OceanDNA-b35375.fa]
[2023-03-18 10:12:21,637] [INFO] Query marker FASTA was written to OceanDNA-b35375/markers.fasta
[2023-03-18 10:12:21,639] [INFO] Task started: Blastn
[2023-03-18 10:12:21,639] [INFO] Running command: blastn -query OceanDNA-b35375/markers.fasta -db /var/lib/cwl/stg8ab802c2-6d79-4691-9210-f468dedd2f20/dqc_reference/reference_markers.fasta -out OceanDNA-b35375/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:12:22,198] [INFO] Task succeeded: Blastn
[2023-03-18 10:12:22,202] [INFO] Selected 19 target genomes.
[2023-03-18 10:12:22,202] [INFO] Target genome list was writen to OceanDNA-b35375/target_genomes.txt
[2023-03-18 10:12:22,215] [INFO] Task started: fastANI
[2023-03-18 10:12:22,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgb11bcd03-744d-4af2-b1d2-8c68939bb9fc/OceanDNA-b35375.fa --refList OceanDNA-b35375/target_genomes.txt --output OceanDNA-b35375/fastani_result.tsv --threads 1
[2023-03-18 10:12:31,923] [INFO] Task succeeded: fastANI
[2023-03-18 10:12:31,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ab802c2-6d79-4691-9210-f468dedd2f20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:12:31,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ab802c2-6d79-4691-9210-f468dedd2f20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:12:31,929] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:12:31,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:12:31,929] [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
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.2341	54	561	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.2078	80	561	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.2058	55	561	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	75.2778	70	561	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	75.2671	71	561	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:12:31,930] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35375/tc_result.tsv
[2023-03-18 10:12:31,931] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:12:31,931] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:12:31,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ab802c2-6d79-4691-9210-f468dedd2f20/dqc_reference/checkm_data
[2023-03-18 10:12:31,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:12:31,955] [INFO] Task started: CheckM
[2023-03-18 10:12:31,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35375/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35375/checkm_input OceanDNA-b35375/checkm_result
[2023-03-18 10:13:00,729] [INFO] Task succeeded: CheckM
[2023-03-18 10:13:00,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:13:00,738] [INFO] ===== Completeness check finished =====
[2023-03-18 10:13:00,738] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:13:00,738] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35375/markers.fasta)
[2023-03-18 10:13:00,739] [INFO] Task started: Blastn
[2023-03-18 10:13:00,739] [INFO] Running command: blastn -query OceanDNA-b35375/markers.fasta -db /var/lib/cwl/stg8ab802c2-6d79-4691-9210-f468dedd2f20/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35375/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:13:01,574] [INFO] Task succeeded: Blastn
[2023-03-18 10:13:01,576] [INFO] Selected 15 target genomes.
[2023-03-18 10:13:01,576] [INFO] Target genome list was writen to OceanDNA-b35375/target_genomes_gtdb.txt
[2023-03-18 10:13:01,613] [INFO] Task started: fastANI
[2023-03-18 10:13:01,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgb11bcd03-744d-4af2-b1d2-8c68939bb9fc/OceanDNA-b35375.fa --refList OceanDNA-b35375/target_genomes_gtdb.txt --output OceanDNA-b35375/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:13:09,758] [INFO] Task succeeded: fastANI
[2023-03-18 10:13:09,762] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:13:09,762] [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_009937625.1	s__GCA-001735895 sp009937625	77.7948	207	561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__GCA-001735895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001735895.1	s__GCA-001735895 sp001735895	77.555	139	561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__GCA-001735895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494335.1	s__S144-22 sp015494335	76.4565	82	561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__S144-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	75.1526	54	561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:13:09,763] [INFO] GTDB search result was written to OceanDNA-b35375/result_gtdb.tsv
[2023-03-18 10:13:09,764] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:13:09,766] [INFO] DFAST_QC result json was written to OceanDNA-b35375/dqc_result.json
[2023-03-18 10:13:09,766] [INFO] DFAST_QC completed!
[2023-03-18 10:13:09,766] [INFO] Total running time: 0h0m60s