[2023-03-17 23:20:45,990] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:20:45,991] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:20:45,991] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e995fc8-c166-44fb-83df-9cd396a3462d/dqc_reference
[2023-03-17 23:20:47,117] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:20:47,117] [INFO] Task started: Prodigal
[2023-03-17 23:20:47,117] [INFO] Running command: cat /var/lib/cwl/stgaa2da4c0-c130-4b5c-b9b0-d03e70671c08/OceanDNA-b15078.fa | prodigal -d OceanDNA-b15078/cds.fna -a OceanDNA-b15078/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:20:55,552] [INFO] Task succeeded: Prodigal
[2023-03-17 23:20:55,553] [INFO] Task started: HMMsearch
[2023-03-17 23:20:55,553] [INFO] Running command: hmmsearch --tblout OceanDNA-b15078/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e995fc8-c166-44fb-83df-9cd396a3462d/dqc_reference/reference_markers.hmm OceanDNA-b15078/protein.faa > /dev/null
[2023-03-17 23:20:55,716] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:20:55,717] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgaa2da4c0-c130-4b5c-b9b0-d03e70671c08/OceanDNA-b15078.fa]
[2023-03-17 23:20:55,733] [INFO] Query marker FASTA was written to OceanDNA-b15078/markers.fasta
[2023-03-17 23:20:55,734] [INFO] Task started: Blastn
[2023-03-17 23:20:55,734] [INFO] Running command: blastn -query OceanDNA-b15078/markers.fasta -db /var/lib/cwl/stg1e995fc8-c166-44fb-83df-9cd396a3462d/dqc_reference/reference_markers.fasta -out OceanDNA-b15078/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:20:56,217] [INFO] Task succeeded: Blastn
[2023-03-17 23:20:56,220] [INFO] Selected 6 target genomes.
[2023-03-17 23:20:56,221] [INFO] Target genome list was writen to OceanDNA-b15078/target_genomes.txt
[2023-03-17 23:20:56,224] [INFO] Task started: fastANI
[2023-03-17 23:20:56,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa2da4c0-c130-4b5c-b9b0-d03e70671c08/OceanDNA-b15078.fa --refList OceanDNA-b15078/target_genomes.txt --output OceanDNA-b15078/fastani_result.tsv --threads 1
[2023-03-17 23:20:59,962] [INFO] Task succeeded: fastANI
[2023-03-17 23:20:59,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e995fc8-c166-44fb-83df-9cd396a3462d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:20:59,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e995fc8-c166-44fb-83df-9cd396a3462d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:20:59,963] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:20:59,963] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:20:59,963] [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
--------------------------------------------------------------------------------
[2023-03-17 23:20:59,964] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15078/tc_result.tsv
[2023-03-17 23:20:59,964] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:20:59,965] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:20:59,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e995fc8-c166-44fb-83df-9cd396a3462d/dqc_reference/checkm_data
[2023-03-17 23:20:59,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:20:59,974] [INFO] Task started: CheckM
[2023-03-17 23:20:59,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15078/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15078/checkm_input OceanDNA-b15078/checkm_result
[2023-03-17 23:21:26,175] [INFO] Task succeeded: CheckM
[2023-03-17 23:21:26,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 5.30%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:21:26,180] [INFO] ===== Completeness check finished =====
[2023-03-17 23:21:26,180] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:21:26,180] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15078/markers.fasta)
[2023-03-17 23:21:26,181] [INFO] Task started: Blastn
[2023-03-17 23:21:26,181] [INFO] Running command: blastn -query OceanDNA-b15078/markers.fasta -db /var/lib/cwl/stg1e995fc8-c166-44fb-83df-9cd396a3462d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15078/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:21:26,799] [INFO] Task succeeded: Blastn
[2023-03-17 23:21:26,799] [INFO] Selected 10 target genomes.
[2023-03-17 23:21:26,799] [INFO] Target genome list was writen to OceanDNA-b15078/target_genomes_gtdb.txt
[2023-03-17 23:21:27,030] [INFO] Task started: fastANI
[2023-03-17 23:21:27,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa2da4c0-c130-4b5c-b9b0-d03e70671c08/OceanDNA-b15078.fa --refList OceanDNA-b15078/target_genomes_gtdb.txt --output OceanDNA-b15078/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:21:32,270] [INFO] Task succeeded: fastANI
[2023-03-17 23:21:32,273] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:21:32,273] [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_014239685.1	s__GCA-2730555 sp014239685	93.4266	366	454	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730555.1	s__GCA-2730555 sp002730555	78.4621	253	454	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.68	99.68	0.93	0.93	2	-
GCA_018650185.1	s__GCA-2730555 sp018650185	77.5558	206	454	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.67	99.66	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-17 23:21:32,274] [INFO] GTDB search result was written to OceanDNA-b15078/result_gtdb.tsv
[2023-03-17 23:21:32,274] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:21:32,275] [INFO] DFAST_QC result json was written to OceanDNA-b15078/dqc_result.json
[2023-03-17 23:21:32,276] [INFO] DFAST_QC completed!
[2023-03-17 23:21:32,276] [INFO] Total running time: 0h0m46s