[2023-03-15 10:52:57,299] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,300] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,300] [INFO] DQC Reference Directory: /var/lib/cwl/stg16984c86-892c-4460-9a9d-8ff927ddebe6/dqc_reference
[2023-03-15 10:52:58,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,866] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,866] [INFO] Running command: cat /var/lib/cwl/stg040e0e26-0430-47b7-aadf-232e1e9453e7/OceanDNA-b5117.fa | prodigal -d OceanDNA-b5117/cds.fna -a OceanDNA-b5117/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:07,472] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:07,473] [INFO] Task started: HMMsearch
[2023-03-15 10:53:07,473] [INFO] Running command: hmmsearch --tblout OceanDNA-b5117/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16984c86-892c-4460-9a9d-8ff927ddebe6/dqc_reference/reference_markers.hmm OceanDNA-b5117/protein.faa > /dev/null
[2023-03-15 10:53:07,652] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:07,653] [INFO] Found 6/6 markers.
[2023-03-15 10:53:07,664] [INFO] Query marker FASTA was written to OceanDNA-b5117/markers.fasta
[2023-03-15 10:53:07,665] [INFO] Task started: Blastn
[2023-03-15 10:53:07,665] [INFO] Running command: blastn -query OceanDNA-b5117/markers.fasta -db /var/lib/cwl/stg16984c86-892c-4460-9a9d-8ff927ddebe6/dqc_reference/reference_markers.fasta -out OceanDNA-b5117/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:08,222] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:08,223] [INFO] Selected 26 target genomes.
[2023-03-15 10:53:08,224] [INFO] Target genome list was writen to OceanDNA-b5117/target_genomes.txt
[2023-03-15 10:53:08,243] [INFO] Task started: fastANI
[2023-03-15 10:53:08,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg040e0e26-0430-47b7-aadf-232e1e9453e7/OceanDNA-b5117.fa --refList OceanDNA-b5117/target_genomes.txt --output OceanDNA-b5117/fastani_result.tsv --threads 1
[2023-03-15 10:53:21,331] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:21,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16984c86-892c-4460-9a9d-8ff927ddebe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:21,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16984c86-892c-4460-9a9d-8ff927ddebe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:21,332] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:21,332] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:53:21,332] [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 10:53:21,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5117/tc_result.tsv
[2023-03-15 10:53:21,332] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:21,333] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:21,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16984c86-892c-4460-9a9d-8ff927ddebe6/dqc_reference/checkm_data
[2023-03-15 10:53:21,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:21,350] [INFO] Task started: CheckM
[2023-03-15 10:53:21,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5117/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5117/checkm_input OceanDNA-b5117/checkm_result
[2023-03-15 10:53:47,657] [INFO] Task succeeded: CheckM
[2023-03-15 10:53:47,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:53:47,660] [INFO] ===== Completeness check finished =====
[2023-03-15 10:53:47,660] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:53:47,660] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5117/markers.fasta)
[2023-03-15 10:53:47,661] [INFO] Task started: Blastn
[2023-03-15 10:53:47,661] [INFO] Running command: blastn -query OceanDNA-b5117/markers.fasta -db /var/lib/cwl/stg16984c86-892c-4460-9a9d-8ff927ddebe6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5117/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:48,571] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:48,572] [INFO] Selected 18 target genomes.
[2023-03-15 10:53:48,572] [INFO] Target genome list was writen to OceanDNA-b5117/target_genomes_gtdb.txt
[2023-03-15 10:53:48,590] [INFO] Task started: fastANI
[2023-03-15 10:53:48,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg040e0e26-0430-47b7-aadf-232e1e9453e7/OceanDNA-b5117.fa --refList OceanDNA-b5117/target_genomes_gtdb.txt --output OceanDNA-b5117/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:53:53,881] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:53,889] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:53:53,890] [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_002711125.1	s__GCA-2711125 sp002711125	93.9785	455	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
GCA_902627575.1	s__GCA-2711125 sp902627575	83.0657	309	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715565.1	s__GCA-2715565 sp002715565	76.6868	93	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2715565	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	76.6689	78	479	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_002693745.1	s__BACL11 sp002693745	76.5283	87	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.4765	109	479	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_905478185.1	s__UWMA-0277 sp905478185	76.4539	100	479	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_002705205.1	s__GCA-2705205 sp002705205	76.4328	76	479	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_014384505.1	s__UWMA-0277 sp014384505	76.219	67	479	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	75.9133	72	479	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_902587125.1	s__GCA-2716345 sp902587125	75.8179	53	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2716345	95.0	98.85	98.45	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-15 10:53:53,890] [INFO] GTDB search result was written to OceanDNA-b5117/result_gtdb.tsv
[2023-03-15 10:53:53,890] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:53:53,891] [INFO] DFAST_QC result json was written to OceanDNA-b5117/dqc_result.json
[2023-03-15 10:53:53,891] [INFO] DFAST_QC completed!
[2023-03-15 10:53:53,891] [INFO] Total running time: 0h0m57s