[2023-03-15 11:51:17,348] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,348] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,349] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4b79470-02fc-4def-8a72-3032c78a2405/dqc_reference
[2023-03-15 11:51:18,953] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,954] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,954] [INFO] Running command: cat /var/lib/cwl/stg9902c8e5-7340-4499-8d82-fe1a5068d108/OceanDNA-b32618.fa | prodigal -d OceanDNA-b32618/cds.fna -a OceanDNA-b32618/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:25,242] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:25,242] [INFO] Task started: HMMsearch
[2023-03-15 11:51:25,242] [INFO] Running command: hmmsearch --tblout OceanDNA-b32618/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4b79470-02fc-4def-8a72-3032c78a2405/dqc_reference/reference_markers.hmm OceanDNA-b32618/protein.faa > /dev/null
[2023-03-15 11:51:25,419] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:25,419] [INFO] Found 6/6 markers.
[2023-03-15 11:51:25,429] [INFO] Query marker FASTA was written to OceanDNA-b32618/markers.fasta
[2023-03-15 11:51:25,429] [INFO] Task started: Blastn
[2023-03-15 11:51:25,430] [INFO] Running command: blastn -query OceanDNA-b32618/markers.fasta -db /var/lib/cwl/stgc4b79470-02fc-4def-8a72-3032c78a2405/dqc_reference/reference_markers.fasta -out OceanDNA-b32618/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:26,051] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:26,052] [INFO] Selected 27 target genomes.
[2023-03-15 11:51:26,052] [INFO] Target genome list was writen to OceanDNA-b32618/target_genomes.txt
[2023-03-15 11:51:26,070] [INFO] Task started: fastANI
[2023-03-15 11:51:26,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg9902c8e5-7340-4499-8d82-fe1a5068d108/OceanDNA-b32618.fa --refList OceanDNA-b32618/target_genomes.txt --output OceanDNA-b32618/fastani_result.tsv --threads 1
[2023-03-15 11:51:45,593] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:45,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4b79470-02fc-4def-8a72-3032c78a2405/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:45,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4b79470-02fc-4def-8a72-3032c78a2405/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:45,599] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:45,599] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:51:45,599] [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
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.8892	55	319	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.4506	54	319	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.1379	52	319	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.9517	50	319	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.6271	53	319	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:51:45,599] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32618/tc_result.tsv
[2023-03-15 11:51:45,599] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:45,599] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:45,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4b79470-02fc-4def-8a72-3032c78a2405/dqc_reference/checkm_data
[2023-03-15 11:51:45,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:45,603] [INFO] Task started: CheckM
[2023-03-15 11:51:45,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32618/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32618/checkm_input OceanDNA-b32618/checkm_result
[2023-03-15 11:52:06,922] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:06,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:06,924] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:06,924] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:06,924] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32618/markers.fasta)
[2023-03-15 11:52:06,924] [INFO] Task started: Blastn
[2023-03-15 11:52:06,924] [INFO] Running command: blastn -query OceanDNA-b32618/markers.fasta -db /var/lib/cwl/stgc4b79470-02fc-4def-8a72-3032c78a2405/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32618/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:08,044] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:08,045] [INFO] Selected 24 target genomes.
[2023-03-15 11:52:08,045] [INFO] Target genome list was writen to OceanDNA-b32618/target_genomes_gtdb.txt
[2023-03-15 11:52:08,070] [INFO] Task started: fastANI
[2023-03-15 11:52:08,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg9902c8e5-7340-4499-8d82-fe1a5068d108/OceanDNA-b32618.fa --refList OceanDNA-b32618/target_genomes_gtdb.txt --output OceanDNA-b32618/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:24,096] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:24,100] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:52:24,100] [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_002686135.1	s__UBA11136 sp002686135	98.7179	276	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA11136;f__UBA11136;g__UBA11136	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016776635.1	s__UBA11136 sp016776635	85.8952	284	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA11136;f__UBA11136;g__UBA11136	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.8453	56	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	76.4524	58	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:24,100] [INFO] GTDB search result was written to OceanDNA-b32618/result_gtdb.tsv
[2023-03-15 11:52:24,100] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:24,101] [INFO] DFAST_QC result json was written to OceanDNA-b32618/dqc_result.json
[2023-03-15 11:52:24,101] [INFO] DFAST_QC completed!
[2023-03-15 11:52:24,101] [INFO] Total running time: 0h1m7s