[2023-03-14 15:08:38,671] [INFO] DFAST_QC pipeline started.
[2023-03-14 15:08:38,671] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 15:08:38,671] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdbe99f9-e1ed-496c-a8c6-73ccd3d4d551/dqc_reference
[2023-03-14 15:08:40,774] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 15:08:40,776] [INFO] Task started: Prodigal
[2023-03-14 15:08:40,777] [INFO] Running command: cat /var/lib/cwl/stga0c34167-c79c-4692-bf1f-7cc149a80d9a/OceanDNA-b2738.fa | prodigal -d OceanDNA-b2738/cds.fna -a OceanDNA-b2738/protein.faa -g 11 -q > /dev/null
[2023-03-14 15:08:47,818] [INFO] Task succeeded: Prodigal
[2023-03-14 15:08:47,818] [INFO] Task started: HMMsearch
[2023-03-14 15:08:47,818] [INFO] Running command: hmmsearch --tblout OceanDNA-b2738/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdbe99f9-e1ed-496c-a8c6-73ccd3d4d551/dqc_reference/reference_markers.hmm OceanDNA-b2738/protein.faa > /dev/null
[2023-03-14 15:08:48,134] [INFO] Task succeeded: HMMsearch
[2023-03-14 15:08:48,135] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga0c34167-c79c-4692-bf1f-7cc149a80d9a/OceanDNA-b2738.fa]
[2023-03-14 15:08:48,146] [INFO] Query marker FASTA was written to OceanDNA-b2738/markers.fasta
[2023-03-14 15:08:48,148] [INFO] Task started: Blastn
[2023-03-14 15:08:48,148] [INFO] Running command: blastn -query OceanDNA-b2738/markers.fasta -db /var/lib/cwl/stgbdbe99f9-e1ed-496c-a8c6-73ccd3d4d551/dqc_reference/reference_markers.fasta -out OceanDNA-b2738/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:08:49,076] [INFO] Task succeeded: Blastn
[2023-03-14 15:08:49,077] [INFO] Selected 27 target genomes.
[2023-03-14 15:08:49,077] [INFO] Target genome list was writen to OceanDNA-b2738/target_genomes.txt
[2023-03-14 15:08:49,136] [INFO] Task started: fastANI
[2023-03-14 15:08:49,136] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c34167-c79c-4692-bf1f-7cc149a80d9a/OceanDNA-b2738.fa --refList OceanDNA-b2738/target_genomes.txt --output OceanDNA-b2738/fastani_result.tsv --threads 1
[2023-03-14 15:09:03,182] [INFO] Task succeeded: fastANI
[2023-03-14 15:09:03,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdbe99f9-e1ed-496c-a8c6-73ccd3d4d551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 15:09:03,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdbe99f9-e1ed-496c-a8c6-73ccd3d4d551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 15:09:03,183] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 15:09:03,183] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 15:09:03,183] [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
--------------------------------------------------------------------------------
[2023-03-14 15:09:03,183] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2738/tc_result.tsv
[2023-03-14 15:09:03,183] [INFO] ===== Taxonomy check completed =====
[2023-03-14 15:09:03,183] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 15:09:03,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdbe99f9-e1ed-496c-a8c6-73ccd3d4d551/dqc_reference/checkm_data
[2023-03-14 15:09:03,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 15:09:03,240] [INFO] Task started: CheckM
[2023-03-14 15:09:03,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2738/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2738/checkm_input OceanDNA-b2738/checkm_result
[2023-03-14 15:09:31,658] [INFO] Task succeeded: CheckM
[2023-03-14 15:09:31,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.31%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 15:09:31,659] [INFO] ===== Completeness check finished =====
[2023-03-14 15:09:31,660] [INFO] ===== Start GTDB Search =====
[2023-03-14 15:09:31,660] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2738/markers.fasta)
[2023-03-14 15:09:31,661] [INFO] Task started: Blastn
[2023-03-14 15:09:31,662] [INFO] Running command: blastn -query OceanDNA-b2738/markers.fasta -db /var/lib/cwl/stgbdbe99f9-e1ed-496c-a8c6-73ccd3d4d551/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2738/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:09:34,276] [INFO] Task succeeded: Blastn
[2023-03-14 15:09:34,277] [INFO] Selected 27 target genomes.
[2023-03-14 15:09:34,277] [INFO] Target genome list was writen to OceanDNA-b2738/target_genomes_gtdb.txt
[2023-03-14 15:09:34,549] [INFO] Task started: fastANI
[2023-03-14 15:09:34,549] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c34167-c79c-4692-bf1f-7cc149a80d9a/OceanDNA-b2738.fa --refList OceanDNA-b2738/target_genomes_gtdb.txt --output OceanDNA-b2738/fastani_result_gtdb.tsv --threads 1
[2023-03-14 15:09:48,302] [INFO] Task succeeded: fastANI
[2023-03-14 15:09:48,305] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 15:09:48,305] [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_018402295.1	s__Pontimonas sp018402295	81.4279	129	278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666065.1	s__Pontimonas sp018666065	79.7473	118	278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857245.1	s__Pontimonas sp017857245	77.7881	55	278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	98.06	96.78	0.86	0.79	3	-
--------------------------------------------------------------------------------
[2023-03-14 15:09:48,305] [INFO] GTDB search result was written to OceanDNA-b2738/result_gtdb.tsv
[2023-03-14 15:09:48,305] [INFO] ===== GTDB Search completed =====
[2023-03-14 15:09:48,306] [INFO] DFAST_QC result json was written to OceanDNA-b2738/dqc_result.json
[2023-03-14 15:09:48,306] [INFO] DFAST_QC completed!
[2023-03-14 15:09:48,306] [INFO] Total running time: 0h1m10s