[2023-03-18 00:28:55,444] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:28:55,444] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:28:55,444] [INFO] DQC Reference Directory: /var/lib/cwl/stg96509950-16ee-4ff9-987f-5a8e0b0792f0/dqc_reference
[2023-03-18 00:28:56,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:28:56,543] [INFO] Task started: Prodigal
[2023-03-18 00:28:56,543] [INFO] Running command: cat /var/lib/cwl/stg83fe3671-e9e1-48bd-a24f-13dd24b53f3f/OceanDNA-b19692.fa | prodigal -d OceanDNA-b19692/cds.fna -a OceanDNA-b19692/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:29:05,464] [INFO] Task succeeded: Prodigal
[2023-03-18 00:29:05,464] [INFO] Task started: HMMsearch
[2023-03-18 00:29:05,464] [INFO] Running command: hmmsearch --tblout OceanDNA-b19692/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96509950-16ee-4ff9-987f-5a8e0b0792f0/dqc_reference/reference_markers.hmm OceanDNA-b19692/protein.faa > /dev/null
[2023-03-18 00:29:05,625] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:29:05,625] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg83fe3671-e9e1-48bd-a24f-13dd24b53f3f/OceanDNA-b19692.fa]
[2023-03-18 00:29:05,638] [INFO] Query marker FASTA was written to OceanDNA-b19692/markers.fasta
[2023-03-18 00:29:05,639] [INFO] Task started: Blastn
[2023-03-18 00:29:05,639] [INFO] Running command: blastn -query OceanDNA-b19692/markers.fasta -db /var/lib/cwl/stg96509950-16ee-4ff9-987f-5a8e0b0792f0/dqc_reference/reference_markers.fasta -out OceanDNA-b19692/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:29:06,121] [INFO] Task succeeded: Blastn
[2023-03-18 00:29:06,121] [INFO] Selected 6 target genomes.
[2023-03-18 00:29:06,121] [INFO] Target genome list was writen to OceanDNA-b19692/target_genomes.txt
[2023-03-18 00:29:06,125] [INFO] Task started: fastANI
[2023-03-18 00:29:06,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg83fe3671-e9e1-48bd-a24f-13dd24b53f3f/OceanDNA-b19692.fa --refList OceanDNA-b19692/target_genomes.txt --output OceanDNA-b19692/fastani_result.tsv --threads 1
[2023-03-18 00:29:08,719] [INFO] Task succeeded: fastANI
[2023-03-18 00:29:08,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96509950-16ee-4ff9-987f-5a8e0b0792f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:29:08,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96509950-16ee-4ff9-987f-5a8e0b0792f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:29:08,720] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:29:08,720] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:29:08,720] [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 00:29:08,720] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19692/tc_result.tsv
[2023-03-18 00:29:08,720] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:29:08,721] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:29:08,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96509950-16ee-4ff9-987f-5a8e0b0792f0/dqc_reference/checkm_data
[2023-03-18 00:29:08,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:29:08,732] [INFO] Task started: CheckM
[2023-03-18 00:29:08,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19692/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19692/checkm_input OceanDNA-b19692/checkm_result
[2023-03-18 00:29:33,657] [INFO] Task succeeded: CheckM
[2023-03-18 00:29:33,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:29:33,660] [INFO] ===== Completeness check finished =====
[2023-03-18 00:29:33,660] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:29:33,660] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19692/markers.fasta)
[2023-03-18 00:29:33,661] [INFO] Task started: Blastn
[2023-03-18 00:29:33,661] [INFO] Running command: blastn -query OceanDNA-b19692/markers.fasta -db /var/lib/cwl/stg96509950-16ee-4ff9-987f-5a8e0b0792f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19692/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:29:34,291] [INFO] Task succeeded: Blastn
[2023-03-18 00:29:34,291] [INFO] Selected 12 target genomes.
[2023-03-18 00:29:34,291] [INFO] Target genome list was writen to OceanDNA-b19692/target_genomes_gtdb.txt
[2023-03-18 00:29:34,303] [INFO] Task started: fastANI
[2023-03-18 00:29:34,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg83fe3671-e9e1-48bd-a24f-13dd24b53f3f/OceanDNA-b19692.fa --refList OceanDNA-b19692/target_genomes_gtdb.txt --output OceanDNA-b19692/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:29:38,098] [INFO] Task succeeded: fastANI
[2023-03-18 00:29:38,102] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:29:38,102] [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_002694025.1	s__GCA-002708715 sp002694025	95.5023	213	534	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002708715	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002691285.1	s__GCA-002708715 sp002691285	78.7318	251	534	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002708715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602795.1	s__GCA-002708715 sp902602795	78.6635	146	534	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002708715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708715.1	s__GCA-002708715 sp002708715	76.7787	124	534	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002708715	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:29:38,102] [INFO] GTDB search result was written to OceanDNA-b19692/result_gtdb.tsv
[2023-03-18 00:29:38,102] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:29:38,103] [INFO] DFAST_QC result json was written to OceanDNA-b19692/dqc_result.json
[2023-03-18 00:29:38,103] [INFO] DFAST_QC completed!
[2023-03-18 00:29:38,103] [INFO] Total running time: 0h0m43s