[2023-03-19 04:11:06,929] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,929] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg77d33b3d-76ae-4d0a-ada8-6ccde890e56d/dqc_reference
[2023-03-19 04:11:08,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,544] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,544] [INFO] Running command: cat /var/lib/cwl/stg6487c06e-fe78-41f3-9dd4-a645c807c684/OceanDNA-b17763.fa | prodigal -d OceanDNA-b17763/cds.fna -a OceanDNA-b17763/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:39,059] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:39,059] [INFO] Task started: HMMsearch
[2023-03-19 04:11:39,059] [INFO] Running command: hmmsearch --tblout OceanDNA-b17763/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77d33b3d-76ae-4d0a-ada8-6ccde890e56d/dqc_reference/reference_markers.hmm OceanDNA-b17763/protein.faa > /dev/null
[2023-03-19 04:11:39,292] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:39,292] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6487c06e-fe78-41f3-9dd4-a645c807c684/OceanDNA-b17763.fa]
[2023-03-19 04:11:39,326] [INFO] Query marker FASTA was written to OceanDNA-b17763/markers.fasta
[2023-03-19 04:11:39,326] [INFO] Task started: Blastn
[2023-03-19 04:11:39,326] [INFO] Running command: blastn -query OceanDNA-b17763/markers.fasta -db /var/lib/cwl/stg77d33b3d-76ae-4d0a-ada8-6ccde890e56d/dqc_reference/reference_markers.fasta -out OceanDNA-b17763/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:39,852] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:39,852] [INFO] Selected 26 target genomes.
[2023-03-19 04:11:39,853] [INFO] Target genome list was writen to OceanDNA-b17763/target_genomes.txt
[2023-03-19 04:11:39,864] [INFO] Task started: fastANI
[2023-03-19 04:11:39,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg6487c06e-fe78-41f3-9dd4-a645c807c684/OceanDNA-b17763.fa --refList OceanDNA-b17763/target_genomes.txt --output OceanDNA-b17763/fastani_result.tsv --threads 1
[2023-03-19 04:11:53,368] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:53,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77d33b3d-76ae-4d0a-ada8-6ccde890e56d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:53,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77d33b3d-76ae-4d0a-ada8-6ccde890e56d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:53,369] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:53,369] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:11:53,369] [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
--------------------------------------------------------------------------------
[2023-03-19 04:11:53,369] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17763/tc_result.tsv
[2023-03-19 04:11:53,369] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:53,369] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:53,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77d33b3d-76ae-4d0a-ada8-6ccde890e56d/dqc_reference/checkm_data
[2023-03-19 04:11:53,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:53,378] [INFO] Task started: CheckM
[2023-03-19 04:11:53,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17763/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17763/checkm_input OceanDNA-b17763/checkm_result
[2023-03-19 04:13:07,279] [INFO] Task succeeded: CheckM
[2023-03-19 04:13:07,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 04:13:07,282] [INFO] ===== Completeness check finished =====
[2023-03-19 04:13:07,283] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:13:07,283] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17763/markers.fasta)
[2023-03-19 04:13:07,283] [INFO] Task started: Blastn
[2023-03-19 04:13:07,283] [INFO] Running command: blastn -query OceanDNA-b17763/markers.fasta -db /var/lib/cwl/stg77d33b3d-76ae-4d0a-ada8-6ccde890e56d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17763/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:13:08,024] [INFO] Task succeeded: Blastn
[2023-03-19 04:13:08,025] [INFO] Selected 26 target genomes.
[2023-03-19 04:13:08,025] [INFO] Target genome list was writen to OceanDNA-b17763/target_genomes_gtdb.txt
[2023-03-19 04:13:08,449] [INFO] Task started: fastANI
[2023-03-19 04:13:08,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg6487c06e-fe78-41f3-9dd4-a645c807c684/OceanDNA-b17763.fa --refList OceanDNA-b17763/target_genomes_gtdb.txt --output OceanDNA-b17763/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:13:24,052] [INFO] Task succeeded: fastANI
[2023-03-19 04:13:24,055] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:13:24,056] [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_002726335.1	s__UBA8231 sp002726335	78.0357	587	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660835.1	s__UBA12574 sp018660835	76.3942	140	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	99.93	99.91	0.98	0.97	7	-
GCA_002712305.1	s__UBA12574 sp002712305	75.9493	136	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	98.27	97.81	0.83	0.79	3	-
GCA_018673255.1	s__UBA12574 sp018673255	75.882	177	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:13:24,056] [INFO] GTDB search result was written to OceanDNA-b17763/result_gtdb.tsv
[2023-03-19 04:13:24,056] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:13:24,056] [INFO] DFAST_QC result json was written to OceanDNA-b17763/dqc_result.json
[2023-03-19 04:13:24,057] [INFO] DFAST_QC completed!
[2023-03-19 04:13:24,057] [INFO] Total running time: 0h2m17s