[2023-03-18 23:36:51,931] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:36:51,931] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:36:51,931] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdb563ea-e00c-4209-886e-966dfa95b294/dqc_reference
[2023-03-18 23:36:53,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:36:53,078] [INFO] Task started: Prodigal
[2023-03-18 23:36:53,078] [INFO] Running command: cat /var/lib/cwl/stgb24fe410-adc4-4628-9a3c-5b401f11a66f/OceanDNA-b4906.fa | prodigal -d OceanDNA-b4906/cds.fna -a OceanDNA-b4906/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:37:02,080] [INFO] Task succeeded: Prodigal
[2023-03-18 23:37:02,081] [INFO] Task started: HMMsearch
[2023-03-18 23:37:02,081] [INFO] Running command: hmmsearch --tblout OceanDNA-b4906/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdb563ea-e00c-4209-886e-966dfa95b294/dqc_reference/reference_markers.hmm OceanDNA-b4906/protein.faa > /dev/null
[2023-03-18 23:37:02,262] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:37:02,263] [INFO] Found 6/6 markers.
[2023-03-18 23:37:02,273] [INFO] Query marker FASTA was written to OceanDNA-b4906/markers.fasta
[2023-03-18 23:37:02,275] [INFO] Task started: Blastn
[2023-03-18 23:37:02,275] [INFO] Running command: blastn -query OceanDNA-b4906/markers.fasta -db /var/lib/cwl/stgfdb563ea-e00c-4209-886e-966dfa95b294/dqc_reference/reference_markers.fasta -out OceanDNA-b4906/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:37:02,845] [INFO] Task succeeded: Blastn
[2023-03-18 23:37:02,846] [INFO] Selected 30 target genomes.
[2023-03-18 23:37:02,846] [INFO] Target genome list was writen to OceanDNA-b4906/target_genomes.txt
[2023-03-18 23:37:02,863] [INFO] Task started: fastANI
[2023-03-18 23:37:02,863] [INFO] Running command: fastANI --query /var/lib/cwl/stgb24fe410-adc4-4628-9a3c-5b401f11a66f/OceanDNA-b4906.fa --refList OceanDNA-b4906/target_genomes.txt --output OceanDNA-b4906/fastani_result.tsv --threads 1
[2023-03-18 23:37:17,736] [INFO] Task succeeded: fastANI
[2023-03-18 23:37:17,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdb563ea-e00c-4209-886e-966dfa95b294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:37:17,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdb563ea-e00c-4209-886e-966dfa95b294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:37:17,737] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:37:17,737] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:37:17,737] [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 23:37:17,737] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4906/tc_result.tsv
[2023-03-18 23:37:17,737] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:37:17,737] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:37:17,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdb563ea-e00c-4209-886e-966dfa95b294/dqc_reference/checkm_data
[2023-03-18 23:37:17,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:37:17,752] [INFO] Task started: CheckM
[2023-03-18 23:37:17,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4906/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4906/checkm_input OceanDNA-b4906/checkm_result
[2023-03-18 23:37:45,764] [INFO] Task succeeded: CheckM
[2023-03-18 23:37:45,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:37:45,766] [INFO] ===== Completeness check finished =====
[2023-03-18 23:37:45,767] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:37:45,767] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4906/markers.fasta)
[2023-03-18 23:37:45,768] [INFO] Task started: Blastn
[2023-03-18 23:37:45,769] [INFO] Running command: blastn -query OceanDNA-b4906/markers.fasta -db /var/lib/cwl/stgfdb563ea-e00c-4209-886e-966dfa95b294/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4906/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:37:46,942] [INFO] Task succeeded: Blastn
[2023-03-18 23:37:46,943] [INFO] Selected 19 target genomes.
[2023-03-18 23:37:46,943] [INFO] Target genome list was writen to OceanDNA-b4906/target_genomes_gtdb.txt
[2023-03-18 23:37:46,996] [INFO] Task started: fastANI
[2023-03-18 23:37:46,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgb24fe410-adc4-4628-9a3c-5b401f11a66f/OceanDNA-b4906.fa --refList OceanDNA-b4906/target_genomes_gtdb.txt --output OceanDNA-b4906/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:37:51,760] [INFO] Task succeeded: fastANI
[2023-03-18 23:37:51,771] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:37:51,771] [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_002730985.1	s__BACL11 sp002730985	97.694	329	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	97.22	97.22	0.84	0.84	2	conclusive
GCA_002693745.1	s__BACL11 sp002693745	78.2106	195	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_905478185.1	s__UWMA-0277 sp905478185	77.8376	202	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_905181635.1	s__UWMA-0277 sp905181635	77.8087	101	491	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_002705205.1	s__GCA-2705205 sp002705205	77.7314	122	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2705205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	77.6726	157	491	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_905478765.1	s__UWMA-0277 sp905478765	77.5628	181	491	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_905612305.1	s__UWMA-0277 sp905612305	77.4315	119	491	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_014384505.1	s__UWMA-0277 sp014384505	77.3404	123	491	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	77.2302	111	491	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_905182255.1	s__UWMA-0277 sp905182255	77.1201	96	491	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	76.9862	109	491	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_902514225.1	s__GCA-002697625 sp902514225	76.8598	52	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018652335.1	s__GCA-2683775 sp018652335	76.8506	116	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683775.1	s__GCA-2683775 sp002683775	76.6448	93	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239655.1	s__GCA-002715885 sp014239655	76.2951	69	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181585.1	s__CAJIYG01 sp905181585	76.179	91	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675825.1	s__GCA-002715885 sp018675825	75.7792	51	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:37:51,771] [INFO] GTDB search result was written to OceanDNA-b4906/result_gtdb.tsv
[2023-03-18 23:37:51,771] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:37:51,772] [INFO] DFAST_QC result json was written to OceanDNA-b4906/dqc_result.json
[2023-03-18 23:37:51,773] [INFO] DFAST_QC completed!
[2023-03-18 23:37:51,773] [INFO] Total running time: 0h0m60s