[2023-03-16 13:57:23,575] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:57:23,575] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:57:23,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg7693ce9e-909f-4c69-a695-319e985f092b/dqc_reference
[2023-03-16 13:57:26,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:57:26,813] [INFO] Task started: Prodigal
[2023-03-16 13:57:26,813] [INFO] Running command: cat /var/lib/cwl/stg75c454e6-2f8a-42e9-a568-ec51113ba973/OceanDNA-b5002.fa | prodigal -d OceanDNA-b5002/cds.fna -a OceanDNA-b5002/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:57:39,128] [INFO] Task succeeded: Prodigal
[2023-03-16 13:57:39,128] [INFO] Task started: HMMsearch
[2023-03-16 13:57:39,129] [INFO] Running command: hmmsearch --tblout OceanDNA-b5002/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7693ce9e-909f-4c69-a695-319e985f092b/dqc_reference/reference_markers.hmm OceanDNA-b5002/protein.faa > /dev/null
[2023-03-16 13:57:39,557] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:57:39,557] [INFO] Found 6/6 markers.
[2023-03-16 13:57:39,568] [INFO] Query marker FASTA was written to OceanDNA-b5002/markers.fasta
[2023-03-16 13:57:39,569] [INFO] Task started: Blastn
[2023-03-16 13:57:39,569] [INFO] Running command: blastn -query OceanDNA-b5002/markers.fasta -db /var/lib/cwl/stg7693ce9e-909f-4c69-a695-319e985f092b/dqc_reference/reference_markers.fasta -out OceanDNA-b5002/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:57:41,121] [INFO] Task succeeded: Blastn
[2023-03-16 13:57:41,122] [INFO] Selected 30 target genomes.
[2023-03-16 13:57:41,122] [INFO] Target genome list was writen to OceanDNA-b5002/target_genomes.txt
[2023-03-16 13:57:41,141] [INFO] Task started: fastANI
[2023-03-16 13:57:41,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c454e6-2f8a-42e9-a568-ec51113ba973/OceanDNA-b5002.fa --refList OceanDNA-b5002/target_genomes.txt --output OceanDNA-b5002/fastani_result.tsv --threads 1
[2023-03-16 13:57:58,550] [INFO] Task succeeded: fastANI
[2023-03-16 13:57:58,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7693ce9e-909f-4c69-a695-319e985f092b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:57:58,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7693ce9e-909f-4c69-a695-319e985f092b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:57:58,551] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:57:58,551] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 13:57:58,551] [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
--------------------------------------------------------------------------------
[2023-03-16 13:57:58,551] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5002/tc_result.tsv
[2023-03-16 13:57:58,551] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:57:58,551] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:57:58,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7693ce9e-909f-4c69-a695-319e985f092b/dqc_reference/checkm_data
[2023-03-16 13:57:58,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:57:58,557] [INFO] Task started: CheckM
[2023-03-16 13:57:58,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5002/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5002/checkm_input OceanDNA-b5002/checkm_result
[2023-03-16 13:58:34,452] [INFO] Task succeeded: CheckM
[2023-03-16 13:58:34,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 13:58:34,454] [INFO] ===== Completeness check finished =====
[2023-03-16 13:58:34,454] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:58:34,454] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5002/markers.fasta)
[2023-03-16 13:58:34,455] [INFO] Task started: Blastn
[2023-03-16 13:58:34,455] [INFO] Running command: blastn -query OceanDNA-b5002/markers.fasta -db /var/lib/cwl/stg7693ce9e-909f-4c69-a695-319e985f092b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5002/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:58:35,454] [INFO] Task succeeded: Blastn
[2023-03-16 13:58:35,455] [INFO] Selected 22 target genomes.
[2023-03-16 13:58:35,455] [INFO] Target genome list was writen to OceanDNA-b5002/target_genomes_gtdb.txt
[2023-03-16 13:58:36,289] [INFO] Task started: fastANI
[2023-03-16 13:58:36,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c454e6-2f8a-42e9-a568-ec51113ba973/OceanDNA-b5002.fa --refList OceanDNA-b5002/target_genomes_gtdb.txt --output OceanDNA-b5002/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:58:44,051] [INFO] Task succeeded: fastANI
[2023-03-16 13:58:44,059] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 13:58:44,059] [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_002689735.1	s__GCA-002715885 sp002689735	97.2334	238	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	96.30	96.30	0.76	0.76	2	conclusive
GCA_902579065.1	s__GCA-002715885 sp902579065	78.5111	167	458	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_014239655.1	s__GCA-002715885 sp014239655	78.3066	185	458	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_018675825.1	s__GCA-002715885 sp018675825	77.9248	134	458	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_002715885.1	s__GCA-002715885 sp002715885	77.3669	118	458	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	77.2817	165	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664745.1	s__UWMA-0277 sp018664745	76.9278	59	458	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	76.4006	84	458	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	76.3287	57	458	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_002728175.1	s__GCA-2697505 sp002728175	76.267	88	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724895.1	s__GCA-2693335 sp002724895	76.2539	90	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2693335	95.0	97.78	97.48	0.81	0.76	3	-
GCA_018647945.1	s__GCA-002697625 sp018647945	76.2157	68	458	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_002697505.1	s__GCA-2697505 sp002697505	76.1065	64	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645865.1	s__UWMA-0277 sp018645865	75.6917	60	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
--------------------------------------------------------------------------------
[2023-03-16 13:58:44,060] [INFO] GTDB search result was written to OceanDNA-b5002/result_gtdb.tsv
[2023-03-16 13:58:44,060] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:58:44,061] [INFO] DFAST_QC result json was written to OceanDNA-b5002/dqc_result.json
[2023-03-16 13:58:44,061] [INFO] DFAST_QC completed!
[2023-03-16 13:58:44,061] [INFO] Total running time: 0h1m20s