[2023-03-18 04:54:25,334] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:54:25,334] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:54:25,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg2978bfb5-8584-4f70-804a-743e6c158b56/dqc_reference
[2023-03-18 04:54:26,988] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:54:26,989] [INFO] Task started: Prodigal
[2023-03-18 04:54:26,989] [INFO] Running command: cat /var/lib/cwl/stgeda9871c-c9ba-4b6c-86d2-467141d3c28c/OceanDNA-b17135.fa | prodigal -d OceanDNA-b17135/cds.fna -a OceanDNA-b17135/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:54:37,578] [INFO] Task succeeded: Prodigal
[2023-03-18 04:54:37,578] [INFO] Task started: HMMsearch
[2023-03-18 04:54:37,578] [INFO] Running command: hmmsearch --tblout OceanDNA-b17135/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2978bfb5-8584-4f70-804a-743e6c158b56/dqc_reference/reference_markers.hmm OceanDNA-b17135/protein.faa > /dev/null
[2023-03-18 04:54:37,741] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:54:37,742] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgeda9871c-c9ba-4b6c-86d2-467141d3c28c/OceanDNA-b17135.fa]
[2023-03-18 04:54:37,762] [INFO] Query marker FASTA was written to OceanDNA-b17135/markers.fasta
[2023-03-18 04:54:37,764] [INFO] Task started: Blastn
[2023-03-18 04:54:37,764] [INFO] Running command: blastn -query OceanDNA-b17135/markers.fasta -db /var/lib/cwl/stg2978bfb5-8584-4f70-804a-743e6c158b56/dqc_reference/reference_markers.fasta -out OceanDNA-b17135/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:54:38,199] [INFO] Task succeeded: Blastn
[2023-03-18 04:54:38,200] [INFO] Selected 9 target genomes.
[2023-03-18 04:54:38,200] [INFO] Target genome list was writen to OceanDNA-b17135/target_genomes.txt
[2023-03-18 04:54:38,207] [INFO] Task started: fastANI
[2023-03-18 04:54:38,207] [INFO] Running command: fastANI --query /var/lib/cwl/stgeda9871c-c9ba-4b6c-86d2-467141d3c28c/OceanDNA-b17135.fa --refList OceanDNA-b17135/target_genomes.txt --output OceanDNA-b17135/fastani_result.tsv --threads 1
[2023-03-18 04:54:45,057] [INFO] Task succeeded: fastANI
[2023-03-18 04:54:45,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2978bfb5-8584-4f70-804a-743e6c158b56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:54:45,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2978bfb5-8584-4f70-804a-743e6c158b56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:54:45,061] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 04:54:45,061] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:54:45,061] [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
Desulfopila aestuarii	strain=DSM 18488	GCA_900143695.1	231440	231440	type	True	97.0942	405	461	95	conclusive
Desulfosediminicola flagellatus	strain=IMCC35005	GCA_005116655.2	2569541	2569541	type	True	77.0416	54	461	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:54:45,061] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17135/tc_result.tsv
[2023-03-18 04:54:45,061] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:54:45,061] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:54:45,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2978bfb5-8584-4f70-804a-743e6c158b56/dqc_reference/checkm_data
[2023-03-18 04:54:45,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:54:45,240] [INFO] Task started: CheckM
[2023-03-18 04:54:45,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17135/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17135/checkm_input OceanDNA-b17135/checkm_result
[2023-03-18 04:55:17,012] [INFO] Task succeeded: CheckM
[2023-03-18 04:55:17,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:55:17,037] [INFO] ===== Completeness check finished =====
[2023-03-18 04:55:17,038] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:55:17,038] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17135/markers.fasta)
[2023-03-18 04:55:17,039] [INFO] Task started: Blastn
[2023-03-18 04:55:17,039] [INFO] Running command: blastn -query OceanDNA-b17135/markers.fasta -db /var/lib/cwl/stg2978bfb5-8584-4f70-804a-743e6c158b56/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17135/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:55:17,494] [INFO] Task succeeded: Blastn
[2023-03-18 04:55:17,502] [INFO] Selected 15 target genomes.
[2023-03-18 04:55:17,503] [INFO] Target genome list was writen to OceanDNA-b17135/target_genomes_gtdb.txt
[2023-03-18 04:55:17,519] [INFO] Task started: fastANI
[2023-03-18 04:55:17,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgeda9871c-c9ba-4b6c-86d2-467141d3c28c/OceanDNA-b17135.fa --refList OceanDNA-b17135/target_genomes_gtdb.txt --output OceanDNA-b17135/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:55:27,145] [INFO] Task succeeded: fastANI
[2023-03-18 04:55:27,148] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:55:27,148] [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
GCF_900143695.1	s__Desulfopila aestuarii	97.0942	405	461	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005116655.2	s__Desulfopila sp005116655	77.0316	55	461	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:55:27,148] [INFO] GTDB search result was written to OceanDNA-b17135/result_gtdb.tsv
[2023-03-18 04:55:27,148] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:55:27,149] [INFO] DFAST_QC result json was written to OceanDNA-b17135/dqc_result.json
[2023-03-18 04:55:27,149] [INFO] DFAST_QC completed!
[2023-03-18 04:55:27,149] [INFO] Total running time: 0h1m2s