[2023-03-17 05:01:06,439] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,439] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,439] [INFO] DQC Reference Directory: /var/lib/cwl/stgca954d11-3d25-4f3e-ab79-886ee6e946a0/dqc_reference
[2023-03-17 05:01:07,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:07,999] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,000] [INFO] Running command: cat /var/lib/cwl/stgd6da217e-6590-443a-8be5-a6e45dd4adab/OceanDNA-b20974.fa | prodigal -d OceanDNA-b20974/cds.fna -a OceanDNA-b20974/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:34,054] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:34,055] [INFO] Task started: HMMsearch
[2023-03-17 05:01:34,055] [INFO] Running command: hmmsearch --tblout OceanDNA-b20974/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca954d11-3d25-4f3e-ab79-886ee6e946a0/dqc_reference/reference_markers.hmm OceanDNA-b20974/protein.faa > /dev/null
[2023-03-17 05:01:34,280] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:34,281] [INFO] Found 6/6 markers.
[2023-03-17 05:01:34,305] [INFO] Query marker FASTA was written to OceanDNA-b20974/markers.fasta
[2023-03-17 05:01:34,305] [INFO] Task started: Blastn
[2023-03-17 05:01:34,305] [INFO] Running command: blastn -query OceanDNA-b20974/markers.fasta -db /var/lib/cwl/stgca954d11-3d25-4f3e-ab79-886ee6e946a0/dqc_reference/reference_markers.fasta -out OceanDNA-b20974/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:34,825] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:34,825] [INFO] Selected 30 target genomes.
[2023-03-17 05:01:34,826] [INFO] Target genome list was writen to OceanDNA-b20974/target_genomes.txt
[2023-03-17 05:01:34,840] [INFO] Task started: fastANI
[2023-03-17 05:01:34,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6da217e-6590-443a-8be5-a6e45dd4adab/OceanDNA-b20974.fa --refList OceanDNA-b20974/target_genomes.txt --output OceanDNA-b20974/fastani_result.tsv --threads 1
[2023-03-17 05:01:58,798] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:58,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca954d11-3d25-4f3e-ab79-886ee6e946a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:58,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca954d11-3d25-4f3e-ab79-886ee6e946a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:58,799] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:01:58,799] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:01:58,799] [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
--------------------------------------------------------------------------------
[2023-03-17 05:01:58,799] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20974/tc_result.tsv
[2023-03-17 05:01:58,799] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:58,799] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:58,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca954d11-3d25-4f3e-ab79-886ee6e946a0/dqc_reference/checkm_data
[2023-03-17 05:01:58,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:58,807] [INFO] Task started: CheckM
[2023-03-17 05:01:58,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20974/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20974/checkm_input OceanDNA-b20974/checkm_result
[2023-03-17 05:03:03,909] [INFO] Task succeeded: CheckM
[2023-03-17 05:03:03,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:03:03,912] [INFO] ===== Completeness check finished =====
[2023-03-17 05:03:03,912] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:03:03,912] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20974/markers.fasta)
[2023-03-17 05:03:03,913] [INFO] Task started: Blastn
[2023-03-17 05:03:03,913] [INFO] Running command: blastn -query OceanDNA-b20974/markers.fasta -db /var/lib/cwl/stgca954d11-3d25-4f3e-ab79-886ee6e946a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20974/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:03:04,618] [INFO] Task succeeded: Blastn
[2023-03-17 05:03:04,619] [INFO] Selected 28 target genomes.
[2023-03-17 05:03:04,619] [INFO] Target genome list was writen to OceanDNA-b20974/target_genomes_gtdb.txt
[2023-03-17 05:03:05,314] [INFO] Task started: fastANI
[2023-03-17 05:03:05,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6da217e-6590-443a-8be5-a6e45dd4adab/OceanDNA-b20974.fa --refList OceanDNA-b20974/target_genomes_gtdb.txt --output OceanDNA-b20974/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:03:23,965] [INFO] Task succeeded: fastANI
[2023-03-17 05:03:23,968] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:03:23,968] [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_002348535.1	s__UBA796 sp002348535	99.6554	1067	1286	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA796;g__UBA796	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002296975.1	s__UBA796 sp002296975	75.6476	66	1286	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA796;g__UBA796	95.0	99.43	99.40	0.83	0.82	3	-
--------------------------------------------------------------------------------
[2023-03-17 05:03:23,968] [INFO] GTDB search result was written to OceanDNA-b20974/result_gtdb.tsv
[2023-03-17 05:03:23,968] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:03:23,969] [INFO] DFAST_QC result json was written to OceanDNA-b20974/dqc_result.json
[2023-03-17 05:03:23,969] [INFO] DFAST_QC completed!
[2023-03-17 05:03:23,969] [INFO] Total running time: 0h2m18s