[2023-03-18 08:55:50,646] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,646] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,646] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6c5532c-a873-46d9-8634-447c566a126d/dqc_reference
[2023-03-18 08:55:51,824] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,824] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,824] [INFO] Running command: cat /var/lib/cwl/stgfce1ff87-3aa2-419a-8540-eda878dd0178/OceanDNA-b8698.fa | prodigal -d OceanDNA-b8698/cds.fna -a OceanDNA-b8698/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:55:57,400] [INFO] Task succeeded: Prodigal
[2023-03-18 08:55:57,400] [INFO] Task started: HMMsearch
[2023-03-18 08:55:57,400] [INFO] Running command: hmmsearch --tblout OceanDNA-b8698/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6c5532c-a873-46d9-8634-447c566a126d/dqc_reference/reference_markers.hmm OceanDNA-b8698/protein.faa > /dev/null
[2023-03-18 08:55:57,588] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:55:57,589] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfce1ff87-3aa2-419a-8540-eda878dd0178/OceanDNA-b8698.fa]
[2023-03-18 08:55:57,598] [INFO] Query marker FASTA was written to OceanDNA-b8698/markers.fasta
[2023-03-18 08:55:57,598] [INFO] Task started: Blastn
[2023-03-18 08:55:57,598] [INFO] Running command: blastn -query OceanDNA-b8698/markers.fasta -db /var/lib/cwl/stgb6c5532c-a873-46d9-8634-447c566a126d/dqc_reference/reference_markers.fasta -out OceanDNA-b8698/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:55:58,116] [INFO] Task succeeded: Blastn
[2023-03-18 08:55:58,117] [INFO] Selected 25 target genomes.
[2023-03-18 08:55:58,117] [INFO] Target genome list was writen to OceanDNA-b8698/target_genomes.txt
[2023-03-18 08:55:58,137] [INFO] Task started: fastANI
[2023-03-18 08:55:58,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgfce1ff87-3aa2-419a-8540-eda878dd0178/OceanDNA-b8698.fa --refList OceanDNA-b8698/target_genomes.txt --output OceanDNA-b8698/fastani_result.tsv --threads 1
[2023-03-18 08:56:12,045] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:12,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6c5532c-a873-46d9-8634-447c566a126d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:12,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6c5532c-a873-46d9-8634-447c566a126d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:12,046] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:12,046] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:56:12,046] [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 08:56:12,046] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8698/tc_result.tsv
[2023-03-18 08:56:12,046] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:12,046] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:12,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6c5532c-a873-46d9-8634-447c566a126d/dqc_reference/checkm_data
[2023-03-18 08:56:12,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:12,073] [INFO] Task started: CheckM
[2023-03-18 08:56:12,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8698/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8698/checkm_input OceanDNA-b8698/checkm_result
[2023-03-18 08:56:31,521] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:31,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:31,524] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:31,524] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:31,524] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8698/markers.fasta)
[2023-03-18 08:56:31,525] [INFO] Task started: Blastn
[2023-03-18 08:56:31,525] [INFO] Running command: blastn -query OceanDNA-b8698/markers.fasta -db /var/lib/cwl/stgb6c5532c-a873-46d9-8634-447c566a126d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8698/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:32,224] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:32,226] [INFO] Selected 14 target genomes.
[2023-03-18 08:56:32,226] [INFO] Target genome list was writen to OceanDNA-b8698/target_genomes_gtdb.txt
[2023-03-18 08:56:32,258] [INFO] Task started: fastANI
[2023-03-18 08:56:32,258] [INFO] Running command: fastANI --query /var/lib/cwl/stgfce1ff87-3aa2-419a-8540-eda878dd0178/OceanDNA-b8698.fa --refList OceanDNA-b8698/target_genomes_gtdb.txt --output OceanDNA-b8698/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:56:35,762] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:35,770] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:56:35,771] [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_902509675.1	s__MED-G13 sp902509675	97.6028	190	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002697255.1	s__MED-G13 sp002697255	82.2272	184	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560045.1	s__MED-G13 sp902560045	81.7235	153	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.04	98.52	0.67	0.66	3	-
GCA_902510475.1	s__MED-G13 sp902510475	81.6081	167	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557655.1	s__MED-G13 sp902557655	81.1547	186	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.84	99.84	0.82	0.82	2	-
GCA_902510415.1	s__MED-G13 sp902510415	79.1103	116	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_902626365.1	s__MED-G13 sp902626365	78.434	106	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.07	96.07	0.74	0.74	2	-
GCA_902517895.1	s__MED-G13 sp902517895	78.4105	108	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519075.1	s__MED-G13 sp902519075	78.2352	114	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518355.1	s__MED-G13 sp902518355	78.1759	117	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_902581145.1	s__MED-G13 sp902581145	77.9779	119	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608795.1	s__MED-G13 sp902608795	77.6579	109	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604715.1	s__MED-G13 sp902604715	77.5839	126	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.66	97.66	0.81	0.81	2	-
GCA_002457735.1	s__MED-G13 sp002457735	76.9304	52	273	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:56:35,771] [INFO] GTDB search result was written to OceanDNA-b8698/result_gtdb.tsv
[2023-03-18 08:56:35,771] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:56:35,773] [INFO] DFAST_QC result json was written to OceanDNA-b8698/dqc_result.json
[2023-03-18 08:56:35,773] [INFO] DFAST_QC completed!
[2023-03-18 08:56:35,773] [INFO] Total running time: 0h0m45s