[2023-03-15 20:34:26,740] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg6beee3b0-04ef-4423-a9dd-137528899a5a/dqc_reference
[2023-03-15 20:34:28,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,468] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,468] [INFO] Running command: cat /var/lib/cwl/stgdb4ea73d-1702-46cf-bdea-c3637280e9f3/OceanDNA-b20952.fa | prodigal -d OceanDNA-b20952/cds.fna -a OceanDNA-b20952/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:49,402] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:49,402] [INFO] Task started: HMMsearch
[2023-03-15 20:34:49,402] [INFO] Running command: hmmsearch --tblout OceanDNA-b20952/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6beee3b0-04ef-4423-a9dd-137528899a5a/dqc_reference/reference_markers.hmm OceanDNA-b20952/protein.faa > /dev/null
[2023-03-15 20:34:49,610] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:49,610] [INFO] Found 6/6 markers.
[2023-03-15 20:34:49,640] [INFO] Query marker FASTA was written to OceanDNA-b20952/markers.fasta
[2023-03-15 20:34:49,640] [INFO] Task started: Blastn
[2023-03-15 20:34:49,640] [INFO] Running command: blastn -query OceanDNA-b20952/markers.fasta -db /var/lib/cwl/stg6beee3b0-04ef-4423-a9dd-137528899a5a/dqc_reference/reference_markers.fasta -out OceanDNA-b20952/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:50,180] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:50,181] [INFO] Selected 37 target genomes.
[2023-03-15 20:34:50,181] [INFO] Target genome list was writen to OceanDNA-b20952/target_genomes.txt
[2023-03-15 20:34:50,201] [INFO] Task started: fastANI
[2023-03-15 20:34:50,202] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb4ea73d-1702-46cf-bdea-c3637280e9f3/OceanDNA-b20952.fa --refList OceanDNA-b20952/target_genomes.txt --output OceanDNA-b20952/fastani_result.tsv --threads 1
[2023-03-15 20:35:16,695] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:16,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6beee3b0-04ef-4423-a9dd-137528899a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:35:16,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6beee3b0-04ef-4423-a9dd-137528899a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:35:16,695] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:35:16,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:35:16,696] [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 20:35:16,696] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20952/tc_result.tsv
[2023-03-15 20:35:16,696] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:35:16,696] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:35:16,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6beee3b0-04ef-4423-a9dd-137528899a5a/dqc_reference/checkm_data
[2023-03-15 20:35:16,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:35:16,704] [INFO] Task started: CheckM
[2023-03-15 20:35:16,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20952/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20952/checkm_input OceanDNA-b20952/checkm_result
[2023-03-15 20:36:09,637] [INFO] Task succeeded: CheckM
[2023-03-15 20:36:09,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.68%
Contamintation: 3.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:36:09,642] [INFO] ===== Completeness check finished =====
[2023-03-15 20:36:09,642] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:36:09,642] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20952/markers.fasta)
[2023-03-15 20:36:09,642] [INFO] Task started: Blastn
[2023-03-15 20:36:09,642] [INFO] Running command: blastn -query OceanDNA-b20952/markers.fasta -db /var/lib/cwl/stg6beee3b0-04ef-4423-a9dd-137528899a5a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20952/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:36:10,423] [INFO] Task succeeded: Blastn
[2023-03-15 20:36:10,424] [INFO] Selected 38 target genomes.
[2023-03-15 20:36:10,424] [INFO] Target genome list was writen to OceanDNA-b20952/target_genomes_gtdb.txt
[2023-03-15 20:36:11,495] [INFO] Task started: fastANI
[2023-03-15 20:36:11,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb4ea73d-1702-46cf-bdea-c3637280e9f3/OceanDNA-b20952.fa --refList OceanDNA-b20952/target_genomes_gtdb.txt --output OceanDNA-b20952/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:36:35,025] [INFO] Task succeeded: fastANI
[2023-03-15 20:36:35,029] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:36:35,029] [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_905480105.1	s__CAJQPC01 sp905480105	99.5666	884	1025	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__CAJQPC01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016717595.1	s__JADKFE01 sp016717595	75.7175	77	1025	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
GCA_016792625.1	s__JAEUKK01 sp016792625	75.4811	51	1025	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343455.1	s__UBA2385 sp002343455	75.4722	62	1025	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:36:35,029] [INFO] GTDB search result was written to OceanDNA-b20952/result_gtdb.tsv
[2023-03-15 20:36:35,030] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:36:35,030] [INFO] DFAST_QC result json was written to OceanDNA-b20952/dqc_result.json
[2023-03-15 20:36:35,030] [INFO] DFAST_QC completed!
[2023-03-15 20:36:35,030] [INFO] Total running time: 0h2m8s