[2023-03-14 11:49:37,369] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:49:37,375] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:49:37,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg80999d5c-1471-4ecf-a44a-b9d2bd41cc46/dqc_reference
[2023-03-14 11:49:38,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:49:38,963] [INFO] Task started: Prodigal
[2023-03-14 11:49:38,963] [INFO] Running command: cat /var/lib/cwl/stgd4c8d8c5-ba75-4b1d-99f3-b3a03e53920d/OceanDNA-b5194.fa | prodigal -d OceanDNA-b5194/cds.fna -a OceanDNA-b5194/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:49:45,181] [INFO] Task succeeded: Prodigal
[2023-03-14 11:49:45,181] [INFO] Task started: HMMsearch
[2023-03-14 11:49:45,181] [INFO] Running command: hmmsearch --tblout OceanDNA-b5194/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80999d5c-1471-4ecf-a44a-b9d2bd41cc46/dqc_reference/reference_markers.hmm OceanDNA-b5194/protein.faa > /dev/null
[2023-03-14 11:49:45,369] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:49:45,370] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd4c8d8c5-ba75-4b1d-99f3-b3a03e53920d/OceanDNA-b5194.fa]
[2023-03-14 11:49:45,404] [INFO] Query marker FASTA was written to OceanDNA-b5194/markers.fasta
[2023-03-14 11:49:45,404] [INFO] Task started: Blastn
[2023-03-14 11:49:45,405] [INFO] Running command: blastn -query OceanDNA-b5194/markers.fasta -db /var/lib/cwl/stg80999d5c-1471-4ecf-a44a-b9d2bd41cc46/dqc_reference/reference_markers.fasta -out OceanDNA-b5194/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:49:45,974] [INFO] Task succeeded: Blastn
[2023-03-14 11:49:45,994] [INFO] Selected 28 target genomes.
[2023-03-14 11:49:45,994] [INFO] Target genome list was writen to OceanDNA-b5194/target_genomes.txt
[2023-03-14 11:49:46,013] [INFO] Task started: fastANI
[2023-03-14 11:49:46,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4c8d8c5-ba75-4b1d-99f3-b3a03e53920d/OceanDNA-b5194.fa --refList OceanDNA-b5194/target_genomes.txt --output OceanDNA-b5194/fastani_result.tsv --threads 1
[2023-03-14 11:50:00,499] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:00,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80999d5c-1471-4ecf-a44a-b9d2bd41cc46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:50:00,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80999d5c-1471-4ecf-a44a-b9d2bd41cc46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:50:00,500] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:50:00,500] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:50:00,500] [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
--------------------------------------------------------------------------------
[2023-03-14 11:50:00,507] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5194/tc_result.tsv
[2023-03-14 11:50:00,519] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:50:00,519] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:50:00,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80999d5c-1471-4ecf-a44a-b9d2bd41cc46/dqc_reference/checkm_data
[2023-03-14 11:50:00,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:50:00,530] [INFO] Task started: CheckM
[2023-03-14 11:50:00,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5194/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5194/checkm_input OceanDNA-b5194/checkm_result
[2023-03-14 11:50:21,959] [INFO] Task succeeded: CheckM
[2023-03-14 11:50:21,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.39%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:50:22,101] [INFO] ===== Completeness check finished =====
[2023-03-14 11:50:22,101] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:50:22,101] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5194/markers.fasta)
[2023-03-14 11:50:22,102] [INFO] Task started: Blastn
[2023-03-14 11:50:22,102] [INFO] Running command: blastn -query OceanDNA-b5194/markers.fasta -db /var/lib/cwl/stg80999d5c-1471-4ecf-a44a-b9d2bd41cc46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5194/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:50:23,046] [INFO] Task succeeded: Blastn
[2023-03-14 11:50:23,074] [INFO] Selected 22 target genomes.
[2023-03-14 11:50:23,074] [INFO] Target genome list was writen to OceanDNA-b5194/target_genomes_gtdb.txt
[2023-03-14 11:50:23,152] [INFO] Task started: fastANI
[2023-03-14 11:50:23,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4c8d8c5-ba75-4b1d-99f3-b3a03e53920d/OceanDNA-b5194.fa --refList OceanDNA-b5194/target_genomes_gtdb.txt --output OceanDNA-b5194/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:50:30,354] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:30,360] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:50:30,360] [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_012960835.1	s__DUAL01 sp012960835	92.4362	242	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381465.1	s__DUAL01 sp014381465	80.7019	230	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170165.1	s__TMED123 sp002170165	78.179	112	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__TMED123	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960805.1	s__UWMA-0277 sp012960805	77.9607	82	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645865.1	s__UWMA-0277 sp018645865	77.2231	66	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
GCA_018647945.1	s__GCA-002697625 sp018647945	77.0706	81	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	99.64	99.58	0.90	0.90	3	-
GCA_014384505.1	s__UWMA-0277 sp014384505	77.0176	66	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664745.1	s__UWMA-0277 sp018664745	76.864	60	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:50:30,400] [INFO] GTDB search result was written to OceanDNA-b5194/result_gtdb.tsv
[2023-03-14 11:50:30,426] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:50:30,435] [INFO] DFAST_QC result json was written to OceanDNA-b5194/dqc_result.json
[2023-03-14 11:50:30,436] [INFO] DFAST_QC completed!
[2023-03-14 11:50:30,436] [INFO] Total running time: 0h0m53s