[2023-03-18 23:27:53,700] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,700] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,700] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbdbac90-aeaf-4906-a8e5-0eadc6aa06d4/dqc_reference
[2023-03-18 23:27:55,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,549] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,550] [INFO] Running command: cat /var/lib/cwl/stga1dcb3fb-589f-4879-a10a-6fe58901c195/OceanDNA-b5195.fa | prodigal -d OceanDNA-b5195/cds.fna -a OceanDNA-b5195/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:27:59,723] [INFO] Task succeeded: Prodigal
[2023-03-18 23:27:59,723] [INFO] Task started: HMMsearch
[2023-03-18 23:27:59,723] [INFO] Running command: hmmsearch --tblout OceanDNA-b5195/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbdbac90-aeaf-4906-a8e5-0eadc6aa06d4/dqc_reference/reference_markers.hmm OceanDNA-b5195/protein.faa > /dev/null
[2023-03-18 23:27:59,880] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:27:59,881] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga1dcb3fb-589f-4879-a10a-6fe58901c195/OceanDNA-b5195.fa]
[2023-03-18 23:27:59,891] [INFO] Query marker FASTA was written to OceanDNA-b5195/markers.fasta
[2023-03-18 23:27:59,891] [INFO] Task started: Blastn
[2023-03-18 23:27:59,891] [INFO] Running command: blastn -query OceanDNA-b5195/markers.fasta -db /var/lib/cwl/stgbbdbac90-aeaf-4906-a8e5-0eadc6aa06d4/dqc_reference/reference_markers.fasta -out OceanDNA-b5195/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:01,473] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:01,474] [INFO] Selected 25 target genomes.
[2023-03-18 23:28:01,474] [INFO] Target genome list was writen to OceanDNA-b5195/target_genomes.txt
[2023-03-18 23:28:01,490] [INFO] Task started: fastANI
[2023-03-18 23:28:01,490] [INFO] Running command: fastANI --query /var/lib/cwl/stga1dcb3fb-589f-4879-a10a-6fe58901c195/OceanDNA-b5195.fa --refList OceanDNA-b5195/target_genomes.txt --output OceanDNA-b5195/fastani_result.tsv --threads 1
[2023-03-18 23:28:15,140] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:15,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbdbac90-aeaf-4906-a8e5-0eadc6aa06d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:15,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbdbac90-aeaf-4906-a8e5-0eadc6aa06d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:15,141] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:15,141] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:28:15,141] [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
--------------------------------------------------------------------------------
[2023-03-18 23:28:15,141] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5195/tc_result.tsv
[2023-03-18 23:28:15,141] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:15,141] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:15,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbdbac90-aeaf-4906-a8e5-0eadc6aa06d4/dqc_reference/checkm_data
[2023-03-18 23:28:15,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:15,192] [INFO] Task started: CheckM
[2023-03-18 23:28:15,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5195/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5195/checkm_input OceanDNA-b5195/checkm_result
[2023-03-18 23:28:32,346] [INFO] Task succeeded: CheckM
[2023-03-18 23:28:32,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:28:32,348] [INFO] ===== Completeness check finished =====
[2023-03-18 23:28:32,348] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:28:32,348] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5195/markers.fasta)
[2023-03-18 23:28:32,349] [INFO] Task started: Blastn
[2023-03-18 23:28:32,349] [INFO] Running command: blastn -query OceanDNA-b5195/markers.fasta -db /var/lib/cwl/stgbbdbac90-aeaf-4906-a8e5-0eadc6aa06d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5195/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:32,818] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:32,819] [INFO] Selected 16 target genomes.
[2023-03-18 23:28:32,819] [INFO] Target genome list was writen to OceanDNA-b5195/target_genomes_gtdb.txt
[2023-03-18 23:28:32,835] [INFO] Task started: fastANI
[2023-03-18 23:28:32,835] [INFO] Running command: fastANI --query /var/lib/cwl/stga1dcb3fb-589f-4879-a10a-6fe58901c195/OceanDNA-b5195.fa --refList OceanDNA-b5195/target_genomes_gtdb.txt --output OceanDNA-b5195/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:28:37,181] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:37,185] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:28:37,185] [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_012960835.1	s__DUAL01 sp012960835	82.0574	134	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381465.1	s__DUAL01 sp014381465	80.454	129	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170165.1	s__TMED123 sp002170165	78.1004	59	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__TMED123	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:28:37,242] [INFO] GTDB search result was written to OceanDNA-b5195/result_gtdb.tsv
[2023-03-18 23:28:37,242] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:28:37,242] [INFO] DFAST_QC result json was written to OceanDNA-b5195/dqc_result.json
[2023-03-18 23:28:37,243] [INFO] DFAST_QC completed!
[2023-03-18 23:28:37,243] [INFO] Total running time: 0h0m44s