[2023-03-18 07:06:20,014] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:20,014] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:20,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg53c918b1-6be0-4bab-a50b-5041c5e8b99f/dqc_reference
[2023-03-18 07:06:21,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:21,127] [INFO] Task started: Prodigal
[2023-03-18 07:06:21,127] [INFO] Running command: cat /var/lib/cwl/stg044a1a2d-9400-477f-b7ae-dc4e57026f2e/OceanDNA-b43700.fa | prodigal -d OceanDNA-b43700/cds.fna -a OceanDNA-b43700/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:27,536] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:27,536] [INFO] Task started: HMMsearch
[2023-03-18 07:06:27,536] [INFO] Running command: hmmsearch --tblout OceanDNA-b43700/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53c918b1-6be0-4bab-a50b-5041c5e8b99f/dqc_reference/reference_markers.hmm OceanDNA-b43700/protein.faa > /dev/null
[2023-03-18 07:06:27,721] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:27,722] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg044a1a2d-9400-477f-b7ae-dc4e57026f2e/OceanDNA-b43700.fa]
[2023-03-18 07:06:27,737] [INFO] Query marker FASTA was written to OceanDNA-b43700/markers.fasta
[2023-03-18 07:06:27,737] [INFO] Task started: Blastn
[2023-03-18 07:06:27,737] [INFO] Running command: blastn -query OceanDNA-b43700/markers.fasta -db /var/lib/cwl/stg53c918b1-6be0-4bab-a50b-5041c5e8b99f/dqc_reference/reference_markers.fasta -out OceanDNA-b43700/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:28,282] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:28,282] [INFO] Selected 17 target genomes.
[2023-03-18 07:06:28,283] [INFO] Target genome list was writen to OceanDNA-b43700/target_genomes.txt
[2023-03-18 07:06:28,292] [INFO] Task started: fastANI
[2023-03-18 07:06:28,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg044a1a2d-9400-477f-b7ae-dc4e57026f2e/OceanDNA-b43700.fa --refList OceanDNA-b43700/target_genomes.txt --output OceanDNA-b43700/fastani_result.tsv --threads 1
[2023-03-18 07:06:37,946] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:37,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53c918b1-6be0-4bab-a50b-5041c5e8b99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:37,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53c918b1-6be0-4bab-a50b-5041c5e8b99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:37,947] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:37,947] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:06:37,947] [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 07:06:37,947] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43700/tc_result.tsv
[2023-03-18 07:06:37,948] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:37,948] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:37,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53c918b1-6be0-4bab-a50b-5041c5e8b99f/dqc_reference/checkm_data
[2023-03-18 07:06:37,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:37,954] [INFO] Task started: CheckM
[2023-03-18 07:06:37,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43700/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43700/checkm_input OceanDNA-b43700/checkm_result
[2023-03-18 07:07:00,401] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:00,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.77%
Contamintation: 10.42%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 07:07:00,404] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:00,404] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:00,404] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43700/markers.fasta)
[2023-03-18 07:07:00,404] [INFO] Task started: Blastn
[2023-03-18 07:07:00,404] [INFO] Running command: blastn -query OceanDNA-b43700/markers.fasta -db /var/lib/cwl/stg53c918b1-6be0-4bab-a50b-5041c5e8b99f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43700/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:01,246] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:01,247] [INFO] Selected 10 target genomes.
[2023-03-18 07:07:01,247] [INFO] Target genome list was writen to OceanDNA-b43700/target_genomes_gtdb.txt
[2023-03-18 07:07:01,464] [INFO] Task started: fastANI
[2023-03-18 07:07:01,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg044a1a2d-9400-477f-b7ae-dc4e57026f2e/OceanDNA-b43700.fa --refList OceanDNA-b43700/target_genomes_gtdb.txt --output OceanDNA-b43700/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:05,836] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:05,841] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:07:05,841] [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_011523045.1	s__UBA868 sp011523045	95.4567	153	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002477475.1	s__UBA868 sp002477475	92.1086	150	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.71	99.58	0.88	0.75	11	-
GCA_002713825.1	s__UBA868 sp002713825	90.0756	109	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694065.1	s__UBA868 sp002694065	89.9153	136	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	97.83	97.76	0.76	0.75	3	-
GCA_002346525.1	s__UBA868 sp002346525	85.0042	109	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845525.1	s__UBA868 sp016845525	84.809	112	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:05,841] [INFO] GTDB search result was written to OceanDNA-b43700/result_gtdb.tsv
[2023-03-18 07:07:05,841] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:05,842] [INFO] DFAST_QC result json was written to OceanDNA-b43700/dqc_result.json
[2023-03-18 07:07:05,842] [INFO] DFAST_QC completed!
[2023-03-18 07:07:05,842] [INFO] Total running time: 0h0m46s