[2023-03-18 05:35:37,312] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg09dbcf1a-df61-4f8a-b1f0-fe209f31d307/dqc_reference
[2023-03-18 05:35:38,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,964] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,964] [INFO] Running command: cat /var/lib/cwl/stgb67b49ab-4050-496a-9da5-85b6f8127677/OceanDNA-b33586.fa | prodigal -d OceanDNA-b33586/cds.fna -a OceanDNA-b33586/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:41,459] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:41,459] [INFO] Task started: HMMsearch
[2023-03-18 05:35:41,459] [INFO] Running command: hmmsearch --tblout OceanDNA-b33586/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09dbcf1a-df61-4f8a-b1f0-fe209f31d307/dqc_reference/reference_markers.hmm OceanDNA-b33586/protein.faa > /dev/null
[2023-03-18 05:35:41,650] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:41,651] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb67b49ab-4050-496a-9da5-85b6f8127677/OceanDNA-b33586.fa]
[2023-03-18 05:35:41,668] [INFO] Query marker FASTA was written to OceanDNA-b33586/markers.fasta
[2023-03-18 05:35:41,670] [INFO] Task started: Blastn
[2023-03-18 05:35:41,670] [INFO] Running command: blastn -query OceanDNA-b33586/markers.fasta -db /var/lib/cwl/stg09dbcf1a-df61-4f8a-b1f0-fe209f31d307/dqc_reference/reference_markers.fasta -out OceanDNA-b33586/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:35:44,658] [INFO] Task succeeded: Blastn
[2023-03-18 05:35:44,662] [INFO] Selected 5 target genomes.
[2023-03-18 05:35:44,663] [INFO] Target genome list was writen to OceanDNA-b33586/target_genomes.txt
[2023-03-18 05:35:44,666] [INFO] Task started: fastANI
[2023-03-18 05:35:44,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgb67b49ab-4050-496a-9da5-85b6f8127677/OceanDNA-b33586.fa --refList OceanDNA-b33586/target_genomes.txt --output OceanDNA-b33586/fastani_result.tsv --threads 1
[2023-03-18 05:35:46,089] [INFO] Task succeeded: fastANI
[2023-03-18 05:35:46,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09dbcf1a-df61-4f8a-b1f0-fe209f31d307/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:35:46,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09dbcf1a-df61-4f8a-b1f0-fe209f31d307/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:35:46,090] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:35:46,090] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:35:46,090] [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 05:35:46,091] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33586/tc_result.tsv
[2023-03-18 05:35:46,092] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:35:46,092] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:35:46,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09dbcf1a-df61-4f8a-b1f0-fe209f31d307/dqc_reference/checkm_data
[2023-03-18 05:35:46,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:35:46,151] [INFO] Task started: CheckM
[2023-03-18 05:35:46,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33586/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33586/checkm_input OceanDNA-b33586/checkm_result
[2023-03-18 05:36:04,068] [INFO] Task succeeded: CheckM
[2023-03-18 05:36:04,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.75%
Contamintation: 1.42%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 05:36:04,122] [INFO] ===== Completeness check finished =====
[2023-03-18 05:36:04,122] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:36:04,122] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33586/markers.fasta)
[2023-03-18 05:36:04,124] [INFO] Task started: Blastn
[2023-03-18 05:36:04,124] [INFO] Running command: blastn -query OceanDNA-b33586/markers.fasta -db /var/lib/cwl/stg09dbcf1a-df61-4f8a-b1f0-fe209f31d307/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33586/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:04,901] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:04,904] [INFO] Selected 11 target genomes.
[2023-03-18 05:36:04,904] [INFO] Target genome list was writen to OceanDNA-b33586/target_genomes_gtdb.txt
[2023-03-18 05:36:04,929] [INFO] Task started: fastANI
[2023-03-18 05:36:04,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgb67b49ab-4050-496a-9da5-85b6f8127677/OceanDNA-b33586.fa --refList OceanDNA-b33586/target_genomes_gtdb.txt --output OceanDNA-b33586/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:36:07,598] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:07,600] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:36:07,600] [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_004214155.1	s__UBA7377 sp004214155	91.7522	83	88	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902586195.1	s__UBA7377 sp902586195	89.8872	56	88	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:36:07,603] [INFO] GTDB search result was written to OceanDNA-b33586/result_gtdb.tsv
[2023-03-18 05:36:07,609] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:36:07,612] [INFO] DFAST_QC result json was written to OceanDNA-b33586/dqc_result.json
[2023-03-18 05:36:07,612] [INFO] DFAST_QC completed!
[2023-03-18 05:36:07,612] [INFO] Total running time: 0h0m30s