[2023-03-15 22:23:01,931] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:23:01,947] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:23:01,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e5ef5c6-1e84-461b-8ed0-b78768c0f669/dqc_reference
[2023-03-15 22:23:03,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:23:03,678] [INFO] Task started: Prodigal
[2023-03-15 22:23:03,678] [INFO] Running command: cat /var/lib/cwl/stg556562a1-b667-4adb-8873-60fef6895482/OceanDNA-b21493.fa | prodigal -d OceanDNA-b21493/cds.fna -a OceanDNA-b21493/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:23:07,861] [INFO] Task succeeded: Prodigal
[2023-03-15 22:23:07,861] [INFO] Task started: HMMsearch
[2023-03-15 22:23:07,861] [INFO] Running command: hmmsearch --tblout OceanDNA-b21493/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e5ef5c6-1e84-461b-8ed0-b78768c0f669/dqc_reference/reference_markers.hmm OceanDNA-b21493/protein.faa > /dev/null
[2023-03-15 22:23:08,020] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:23:08,021] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg556562a1-b667-4adb-8873-60fef6895482/OceanDNA-b21493.fa]
[2023-03-15 22:23:08,026] [INFO] Query marker FASTA was written to OceanDNA-b21493/markers.fasta
[2023-03-15 22:23:08,027] [INFO] Task started: Blastn
[2023-03-15 22:23:08,027] [INFO] Running command: blastn -query OceanDNA-b21493/markers.fasta -db /var/lib/cwl/stg5e5ef5c6-1e84-461b-8ed0-b78768c0f669/dqc_reference/reference_markers.fasta -out OceanDNA-b21493/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:08,786] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:08,787] [INFO] Selected 13 target genomes.
[2023-03-15 22:23:08,787] [INFO] Target genome list was writen to OceanDNA-b21493/target_genomes.txt
[2023-03-15 22:23:08,797] [INFO] Task started: fastANI
[2023-03-15 22:23:08,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg556562a1-b667-4adb-8873-60fef6895482/OceanDNA-b21493.fa --refList OceanDNA-b21493/target_genomes.txt --output OceanDNA-b21493/fastani_result.tsv --threads 1
[2023-03-15 22:23:13,426] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:13,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e5ef5c6-1e84-461b-8ed0-b78768c0f669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:23:13,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e5ef5c6-1e84-461b-8ed0-b78768c0f669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:23:13,427] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:23:13,427] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:23:13,427] [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
--------------------------------------------------------------------------------
[2023-03-15 22:23:13,427] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21493/tc_result.tsv
[2023-03-15 22:23:13,427] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:23:13,427] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:23:13,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e5ef5c6-1e84-461b-8ed0-b78768c0f669/dqc_reference/checkm_data
[2023-03-15 22:23:13,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:23:13,432] [INFO] Task started: CheckM
[2023-03-15 22:23:13,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21493/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21493/checkm_input OceanDNA-b21493/checkm_result
[2023-03-15 22:23:30,158] [INFO] Task succeeded: CheckM
[2023-03-15 22:23:30,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 22:23:30,160] [INFO] ===== Completeness check finished =====
[2023-03-15 22:23:30,160] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:23:30,160] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21493/markers.fasta)
[2023-03-15 22:23:30,160] [INFO] Task started: Blastn
[2023-03-15 22:23:30,161] [INFO] Running command: blastn -query OceanDNA-b21493/markers.fasta -db /var/lib/cwl/stg5e5ef5c6-1e84-461b-8ed0-b78768c0f669/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21493/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:30,806] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:30,807] [INFO] Selected 15 target genomes.
[2023-03-15 22:23:30,807] [INFO] Target genome list was writen to OceanDNA-b21493/target_genomes_gtdb.txt
[2023-03-15 22:23:30,815] [INFO] Task started: fastANI
[2023-03-15 22:23:30,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg556562a1-b667-4adb-8873-60fef6895482/OceanDNA-b21493.fa --refList OceanDNA-b21493/target_genomes_gtdb.txt --output OceanDNA-b21493/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:23:33,449] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:33,453] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:23:33,453] [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_018656655.1	s__XYD1-37-29 sp018656655	99.5686	194	221	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__XYD1-37-29	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018656065.1	s__XYD1-37-29 sp018656065	85.0961	167	221	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__XYD1-37-29	95.0	99.99	99.99	0.98	0.98	2	-
GCA_018669975.1	s__JABHSK01 sp018669975	77.8947	58	221	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__JABHSK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001818495.1	s__XYD1-37-29 sp001818495	77.5703	84	221	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__XYD1-37-29	95.0	99.96	99.96	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-15 22:23:33,453] [INFO] GTDB search result was written to OceanDNA-b21493/result_gtdb.tsv
[2023-03-15 22:23:33,453] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:23:33,454] [INFO] DFAST_QC result json was written to OceanDNA-b21493/dqc_result.json
[2023-03-15 22:23:33,454] [INFO] DFAST_QC completed!
[2023-03-15 22:23:33,454] [INFO] Total running time: 0h0m32s