[2023-03-15 14:40:36,534] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:40:36,534] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:40:36,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg905f5dba-b4b7-4c12-b0e1-942ad621fdfe/dqc_reference
[2023-03-15 14:40:37,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:40:37,684] [INFO] Task started: Prodigal
[2023-03-15 14:40:37,684] [INFO] Running command: cat /var/lib/cwl/stg5f37919e-c06f-4d14-bd91-2d334f3efe28/OceanDNA-b34275.fa | prodigal -d OceanDNA-b34275/cds.fna -a OceanDNA-b34275/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:40:57,253] [INFO] Task succeeded: Prodigal
[2023-03-15 14:40:57,253] [INFO] Task started: HMMsearch
[2023-03-15 14:40:57,253] [INFO] Running command: hmmsearch --tblout OceanDNA-b34275/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg905f5dba-b4b7-4c12-b0e1-942ad621fdfe/dqc_reference/reference_markers.hmm OceanDNA-b34275/protein.faa > /dev/null
[2023-03-15 14:40:57,457] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:40:57,458] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5f37919e-c06f-4d14-bd91-2d334f3efe28/OceanDNA-b34275.fa]
[2023-03-15 14:40:57,482] [INFO] Query marker FASTA was written to OceanDNA-b34275/markers.fasta
[2023-03-15 14:40:57,483] [INFO] Task started: Blastn
[2023-03-15 14:40:57,483] [INFO] Running command: blastn -query OceanDNA-b34275/markers.fasta -db /var/lib/cwl/stg905f5dba-b4b7-4c12-b0e1-942ad621fdfe/dqc_reference/reference_markers.fasta -out OceanDNA-b34275/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:40:57,999] [INFO] Task succeeded: Blastn
[2023-03-15 14:40:57,999] [INFO] Selected 25 target genomes.
[2023-03-15 14:40:58,000] [INFO] Target genome list was writen to OceanDNA-b34275/target_genomes.txt
[2023-03-15 14:40:58,014] [INFO] Task started: fastANI
[2023-03-15 14:40:58,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f37919e-c06f-4d14-bd91-2d334f3efe28/OceanDNA-b34275.fa --refList OceanDNA-b34275/target_genomes.txt --output OceanDNA-b34275/fastani_result.tsv --threads 1
[2023-03-15 14:41:13,015] [INFO] Task succeeded: fastANI
[2023-03-15 14:41:13,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg905f5dba-b4b7-4c12-b0e1-942ad621fdfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:41:13,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg905f5dba-b4b7-4c12-b0e1-942ad621fdfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:41:13,020] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:41:13,020] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:41:13,020] [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
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	76.6849	51	1163	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	76.2151	52	1163	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:41:13,034] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34275/tc_result.tsv
[2023-03-15 14:41:13,035] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:41:13,035] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:41:13,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg905f5dba-b4b7-4c12-b0e1-942ad621fdfe/dqc_reference/checkm_data
[2023-03-15 14:41:13,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:41:13,065] [INFO] Task started: CheckM
[2023-03-15 14:41:13,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34275/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34275/checkm_input OceanDNA-b34275/checkm_result
[2023-03-15 14:42:04,109] [INFO] Task succeeded: CheckM
[2023-03-15 14:42:04,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:42:04,130] [INFO] ===== Completeness check finished =====
[2023-03-15 14:42:04,130] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:42:04,130] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34275/markers.fasta)
[2023-03-15 14:42:04,132] [INFO] Task started: Blastn
[2023-03-15 14:42:04,132] [INFO] Running command: blastn -query OceanDNA-b34275/markers.fasta -db /var/lib/cwl/stg905f5dba-b4b7-4c12-b0e1-942ad621fdfe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34275/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:42:04,814] [INFO] Task succeeded: Blastn
[2023-03-15 14:42:04,816] [INFO] Selected 24 target genomes.
[2023-03-15 14:42:04,816] [INFO] Target genome list was writen to OceanDNA-b34275/target_genomes_gtdb.txt
[2023-03-15 14:42:04,942] [INFO] Task started: fastANI
[2023-03-15 14:42:04,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f37919e-c06f-4d14-bd91-2d334f3efe28/OceanDNA-b34275.fa --refList OceanDNA-b34275/target_genomes_gtdb.txt --output OceanDNA-b34275/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:42:19,934] [INFO] Task succeeded: fastANI
[2023-03-15 14:42:19,937] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:42:19,937] [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_000172635.2	s__Alteromonas macleodii	76.2151	52	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_000808575.1	s__Alteromonas marina	76.0828	62	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 14:42:19,944] [INFO] GTDB search result was written to OceanDNA-b34275/result_gtdb.tsv
[2023-03-15 14:42:19,945] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:42:19,946] [INFO] DFAST_QC result json was written to OceanDNA-b34275/dqc_result.json
[2023-03-15 14:42:19,946] [INFO] DFAST_QC completed!
[2023-03-15 14:42:19,946] [INFO] Total running time: 0h1m43s