[2023-03-16 08:22:25,415] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:22:25,416] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:22:25,416] [INFO] DQC Reference Directory: /var/lib/cwl/stgae058df6-e0c5-44e0-9000-b4d2c015b5fd/dqc_reference
[2023-03-16 08:22:27,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:22:27,101] [INFO] Task started: Prodigal
[2023-03-16 08:22:27,102] [INFO] Running command: cat /var/lib/cwl/stg7250329b-59b0-43c7-ba4f-bf53e3d244ed/OceanDNA-b12754.fa | prodigal -d OceanDNA-b12754/cds.fna -a OceanDNA-b12754/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:22:37,986] [INFO] Task succeeded: Prodigal
[2023-03-16 08:22:37,987] [INFO] Task started: HMMsearch
[2023-03-16 08:22:37,987] [INFO] Running command: hmmsearch --tblout OceanDNA-b12754/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae058df6-e0c5-44e0-9000-b4d2c015b5fd/dqc_reference/reference_markers.hmm OceanDNA-b12754/protein.faa > /dev/null
[2023-03-16 08:22:38,153] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:22:38,154] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7250329b-59b0-43c7-ba4f-bf53e3d244ed/OceanDNA-b12754.fa]
[2023-03-16 08:22:38,176] [INFO] Query marker FASTA was written to OceanDNA-b12754/markers.fasta
[2023-03-16 08:22:38,177] [INFO] Task started: Blastn
[2023-03-16 08:22:38,177] [INFO] Running command: blastn -query OceanDNA-b12754/markers.fasta -db /var/lib/cwl/stgae058df6-e0c5-44e0-9000-b4d2c015b5fd/dqc_reference/reference_markers.fasta -out OceanDNA-b12754/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:38,702] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:38,706] [INFO] Selected 30 target genomes.
[2023-03-16 08:22:38,706] [INFO] Target genome list was writen to OceanDNA-b12754/target_genomes.txt
[2023-03-16 08:22:38,724] [INFO] Task started: fastANI
[2023-03-16 08:22:38,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg7250329b-59b0-43c7-ba4f-bf53e3d244ed/OceanDNA-b12754.fa --refList OceanDNA-b12754/target_genomes.txt --output OceanDNA-b12754/fastani_result.tsv --threads 1
[2023-03-16 08:22:56,846] [INFO] Task succeeded: fastANI
[2023-03-16 08:22:56,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae058df6-e0c5-44e0-9000-b4d2c015b5fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:22:56,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae058df6-e0c5-44e0-9000-b4d2c015b5fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:22:56,847] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:22:56,847] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:22:56,847] [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
--------------------------------------------------------------------------------
[2023-03-16 08:22:56,852] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12754/tc_result.tsv
[2023-03-16 08:22:56,854] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:22:56,854] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:22:56,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae058df6-e0c5-44e0-9000-b4d2c015b5fd/dqc_reference/checkm_data
[2023-03-16 08:22:56,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:22:56,922] [INFO] Task started: CheckM
[2023-03-16 08:22:56,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12754/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12754/checkm_input OceanDNA-b12754/checkm_result
[2023-03-16 08:23:28,521] [INFO] Task succeeded: CheckM
[2023-03-16 08:23:28,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:23:28,525] [INFO] ===== Completeness check finished =====
[2023-03-16 08:23:28,525] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:23:28,526] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12754/markers.fasta)
[2023-03-16 08:23:28,527] [INFO] Task started: Blastn
[2023-03-16 08:23:28,527] [INFO] Running command: blastn -query OceanDNA-b12754/markers.fasta -db /var/lib/cwl/stgae058df6-e0c5-44e0-9000-b4d2c015b5fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12754/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:23:29,244] [INFO] Task succeeded: Blastn
[2023-03-16 08:23:29,245] [INFO] Selected 27 target genomes.
[2023-03-16 08:23:29,245] [INFO] Target genome list was writen to OceanDNA-b12754/target_genomes_gtdb.txt
[2023-03-16 08:23:29,312] [INFO] Task started: fastANI
[2023-03-16 08:23:29,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg7250329b-59b0-43c7-ba4f-bf53e3d244ed/OceanDNA-b12754.fa --refList OceanDNA-b12754/target_genomes_gtdb.txt --output OceanDNA-b12754/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:23:40,751] [INFO] Task succeeded: fastANI
[2023-03-16 08:23:40,755] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:23:40,755] [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_016779945.1	s__UBA9320 sp016779945	79.7292	321	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402155.1	s__UBA9320 sp018402155	76.4859	50	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857855.1	s__UBA9320 sp003516975	76.3332	51	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	99.31	99.21	0.89	0.84	3	-
GCA_002746305.1	s__UBA9320 sp002746305	76.0899	68	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042025.1	s__UBA9320 sp013042025	75.9961	50	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:23:40,755] [INFO] GTDB search result was written to OceanDNA-b12754/result_gtdb.tsv
[2023-03-16 08:23:40,756] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:23:40,756] [INFO] DFAST_QC result json was written to OceanDNA-b12754/dqc_result.json
[2023-03-16 08:23:40,756] [INFO] DFAST_QC completed!
[2023-03-16 08:23:40,756] [INFO] Total running time: 0h1m15s