[2023-03-15 13:54:30,577] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:54:30,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:54:30,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fa388c5-5ef4-4458-a2a1-d7e078203e29/dqc_reference
[2023-03-15 13:54:31,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:54:31,795] [INFO] Task started: Prodigal
[2023-03-15 13:54:31,795] [INFO] Running command: cat /var/lib/cwl/stge476ae17-f315-4479-9c5d-0e8d7e274536/OceanDNA-b24719.fa | prodigal -d OceanDNA-b24719/cds.fna -a OceanDNA-b24719/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:54:48,274] [INFO] Task succeeded: Prodigal
[2023-03-15 13:54:48,274] [INFO] Task started: HMMsearch
[2023-03-15 13:54:48,274] [INFO] Running command: hmmsearch --tblout OceanDNA-b24719/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fa388c5-5ef4-4458-a2a1-d7e078203e29/dqc_reference/reference_markers.hmm OceanDNA-b24719/protein.faa > /dev/null
[2023-03-15 13:54:48,456] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:54:48,457] [INFO] Found 6/6 markers.
[2023-03-15 13:54:48,490] [INFO] Query marker FASTA was written to OceanDNA-b24719/markers.fasta
[2023-03-15 13:54:48,491] [INFO] Task started: Blastn
[2023-03-15 13:54:48,491] [INFO] Running command: blastn -query OceanDNA-b24719/markers.fasta -db /var/lib/cwl/stg2fa388c5-5ef4-4458-a2a1-d7e078203e29/dqc_reference/reference_markers.fasta -out OceanDNA-b24719/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:54:49,175] [INFO] Task succeeded: Blastn
[2023-03-15 13:54:49,180] [INFO] Selected 33 target genomes.
[2023-03-15 13:54:49,181] [INFO] Target genome list was writen to OceanDNA-b24719/target_genomes.txt
[2023-03-15 13:54:49,195] [INFO] Task started: fastANI
[2023-03-15 13:54:49,195] [INFO] Running command: fastANI --query /var/lib/cwl/stge476ae17-f315-4479-9c5d-0e8d7e274536/OceanDNA-b24719.fa --refList OceanDNA-b24719/target_genomes.txt --output OceanDNA-b24719/fastani_result.tsv --threads 1
[2023-03-15 13:55:14,072] [INFO] Task succeeded: fastANI
[2023-03-15 13:55:14,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fa388c5-5ef4-4458-a2a1-d7e078203e29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:55:14,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fa388c5-5ef4-4458-a2a1-d7e078203e29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:55:14,076] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:55:14,076] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:55:14,076] [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
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.4443	50	851	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.0918	59	851	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.0809	60	851	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:55:14,077] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24719/tc_result.tsv
[2023-03-15 13:55:14,077] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:55:14,077] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:55:14,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fa388c5-5ef4-4458-a2a1-d7e078203e29/dqc_reference/checkm_data
[2023-03-15 13:55:14,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:55:14,085] [INFO] Task started: CheckM
[2023-03-15 13:55:14,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24719/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24719/checkm_input OceanDNA-b24719/checkm_result
[2023-03-15 13:55:56,897] [INFO] Task succeeded: CheckM
[2023-03-15 13:55:56,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:55:56,931] [INFO] ===== Completeness check finished =====
[2023-03-15 13:55:56,931] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:55:56,931] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24719/markers.fasta)
[2023-03-15 13:55:56,932] [INFO] Task started: Blastn
[2023-03-15 13:55:56,932] [INFO] Running command: blastn -query OceanDNA-b24719/markers.fasta -db /var/lib/cwl/stg2fa388c5-5ef4-4458-a2a1-d7e078203e29/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24719/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:55:58,162] [INFO] Task succeeded: Blastn
[2023-03-15 13:55:58,169] [INFO] Selected 15 target genomes.
[2023-03-15 13:55:58,169] [INFO] Target genome list was writen to OceanDNA-b24719/target_genomes_gtdb.txt
[2023-03-15 13:55:58,211] [INFO] Task started: fastANI
[2023-03-15 13:55:58,211] [INFO] Running command: fastANI --query /var/lib/cwl/stge476ae17-f315-4479-9c5d-0e8d7e274536/OceanDNA-b24719.fa --refList OceanDNA-b24719/target_genomes_gtdb.txt --output OceanDNA-b24719/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:56:07,285] [INFO] Task succeeded: fastANI
[2023-03-15 13:56:07,289] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:56:07,289] [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_003524565.1	s__UBA2020 sp003524565	81.6755	428	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002334985.1	s__UBA2020 sp002334985	81.6175	492	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794125.1	s__UBA2020 sp016794125	77.498	260	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124645.1	s__UBA2020 sp016124645	76.6883	163	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297545.1	s__UBA2020 sp004297545	76.6035	168	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:56:07,290] [INFO] GTDB search result was written to OceanDNA-b24719/result_gtdb.tsv
[2023-03-15 13:56:07,290] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:56:07,291] [INFO] DFAST_QC result json was written to OceanDNA-b24719/dqc_result.json
[2023-03-15 13:56:07,292] [INFO] DFAST_QC completed!
[2023-03-15 13:56:07,292] [INFO] Total running time: 0h1m37s