[2023-03-16 03:23:48,510] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:48,510] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:48,511] [INFO] DQC Reference Directory: /var/lib/cwl/stg82de64bc-ccdb-4455-9aec-670b6805d9ff/dqc_reference
[2023-03-16 03:23:50,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,645] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,645] [INFO] Running command: cat /var/lib/cwl/stg3829da83-35b0-4939-a02a-a6f8cb0d6946/OceanDNA-b15232.fa | prodigal -d OceanDNA-b15232/cds.fna -a OceanDNA-b15232/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:02,169] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:02,169] [INFO] Task started: HMMsearch
[2023-03-16 03:24:02,169] [INFO] Running command: hmmsearch --tblout OceanDNA-b15232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82de64bc-ccdb-4455-9aec-670b6805d9ff/dqc_reference/reference_markers.hmm OceanDNA-b15232/protein.faa > /dev/null
[2023-03-16 03:24:02,365] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:02,366] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3829da83-35b0-4939-a02a-a6f8cb0d6946/OceanDNA-b15232.fa]
[2023-03-16 03:24:02,382] [INFO] Query marker FASTA was written to OceanDNA-b15232/markers.fasta
[2023-03-16 03:24:02,382] [INFO] Task started: Blastn
[2023-03-16 03:24:02,382] [INFO] Running command: blastn -query OceanDNA-b15232/markers.fasta -db /var/lib/cwl/stg82de64bc-ccdb-4455-9aec-670b6805d9ff/dqc_reference/reference_markers.fasta -out OceanDNA-b15232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:02,903] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:02,903] [INFO] Selected 15 target genomes.
[2023-03-16 03:24:02,904] [INFO] Target genome list was writen to OceanDNA-b15232/target_genomes.txt
[2023-03-16 03:24:02,914] [INFO] Task started: fastANI
[2023-03-16 03:24:02,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg3829da83-35b0-4939-a02a-a6f8cb0d6946/OceanDNA-b15232.fa --refList OceanDNA-b15232/target_genomes.txt --output OceanDNA-b15232/fastani_result.tsv --threads 1
[2023-03-16 03:24:13,429] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:13,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82de64bc-ccdb-4455-9aec-670b6805d9ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:13,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82de64bc-ccdb-4455-9aec-670b6805d9ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:13,429] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:13,430] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:13,430] [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
--------------------------------------------------------------------------------
[2023-03-16 03:24:13,430] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15232/tc_result.tsv
[2023-03-16 03:24:13,430] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:13,430] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:13,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82de64bc-ccdb-4455-9aec-670b6805d9ff/dqc_reference/checkm_data
[2023-03-16 03:24:13,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:13,436] [INFO] Task started: CheckM
[2023-03-16 03:24:13,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15232/checkm_input OceanDNA-b15232/checkm_result
[2023-03-16 03:24:45,726] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:45,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 3.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-16 03:24:45,729] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:45,729] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:45,729] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15232/markers.fasta)
[2023-03-16 03:24:45,729] [INFO] Task started: Blastn
[2023-03-16 03:24:45,729] [INFO] Running command: blastn -query OceanDNA-b15232/markers.fasta -db /var/lib/cwl/stg82de64bc-ccdb-4455-9aec-670b6805d9ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:46,446] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:46,447] [INFO] Selected 8 target genomes.
[2023-03-16 03:24:46,447] [INFO] Target genome list was writen to OceanDNA-b15232/target_genomes_gtdb.txt
[2023-03-16 03:24:46,676] [INFO] Task started: fastANI
[2023-03-16 03:24:46,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg3829da83-35b0-4939-a02a-a6f8cb0d6946/OceanDNA-b15232.fa --refList OceanDNA-b15232/target_genomes_gtdb.txt --output OceanDNA-b15232/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:49,831] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:49,837] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:24:49,837] [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_009391845.1	s__UBA6627 sp009391845	79.6056	113	631	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__UBA6627	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700215.1	s__UBA6955 sp018700215	77.9765	167	631	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__UBA6955	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692765.1	s__SHYQ01 sp009692765	77.2064	76	631	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SHYQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379925.1	s__WHSU01 sp009379925	77.1739	132	631	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__WHSU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866055.1	s__VGNK01 sp016866055	77.0285	155	631	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VGNK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917615.1	s__SHYQ01 sp903917615	76.8382	101	631	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SHYQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840675.1	s__W-Chloroflexi-9 sp002840675	76.717	116	631	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__W-Chloroflexi-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009839925.1	s__VXMT01 sp009839925	76.4072	125	631	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:49,837] [INFO] GTDB search result was written to OceanDNA-b15232/result_gtdb.tsv
[2023-03-16 03:24:49,837] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:49,838] [INFO] DFAST_QC result json was written to OceanDNA-b15232/dqc_result.json
[2023-03-16 03:24:49,838] [INFO] DFAST_QC completed!
[2023-03-16 03:24:49,838] [INFO] Total running time: 0h1m1s