[2023-03-17 15:09:40,834] [INFO] DFAST_QC pipeline started.
[2023-03-17 15:09:40,834] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 15:09:40,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg695b7c6e-e37b-4e1b-9cd7-7fed63e3a853/dqc_reference
[2023-03-17 15:09:42,013] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 15:09:42,038] [INFO] Task started: Prodigal
[2023-03-17 15:09:42,038] [INFO] Running command: cat /var/lib/cwl/stgb1e481ae-7f82-4cdf-9c02-0f5d556ced7a/OceanDNA-b24428.fa | prodigal -d OceanDNA-b24428/cds.fna -a OceanDNA-b24428/protein.faa -g 11 -q > /dev/null
[2023-03-17 15:09:50,807] [INFO] Task succeeded: Prodigal
[2023-03-17 15:09:50,807] [INFO] Task started: HMMsearch
[2023-03-17 15:09:50,807] [INFO] Running command: hmmsearch --tblout OceanDNA-b24428/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg695b7c6e-e37b-4e1b-9cd7-7fed63e3a853/dqc_reference/reference_markers.hmm OceanDNA-b24428/protein.faa > /dev/null
[2023-03-17 15:09:50,979] [INFO] Task succeeded: HMMsearch
[2023-03-17 15:09:50,979] [INFO] Found 6/6 markers.
[2023-03-17 15:09:50,986] [INFO] Query marker FASTA was written to OceanDNA-b24428/markers.fasta
[2023-03-17 15:09:50,986] [INFO] Task started: Blastn
[2023-03-17 15:09:50,986] [INFO] Running command: blastn -query OceanDNA-b24428/markers.fasta -db /var/lib/cwl/stg695b7c6e-e37b-4e1b-9cd7-7fed63e3a853/dqc_reference/reference_markers.fasta -out OceanDNA-b24428/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:09:51,629] [INFO] Task succeeded: Blastn
[2023-03-17 15:09:51,630] [INFO] Selected 20 target genomes.
[2023-03-17 15:09:51,630] [INFO] Target genome list was writen to OceanDNA-b24428/target_genomes.txt
[2023-03-17 15:09:51,642] [INFO] Task started: fastANI
[2023-03-17 15:09:51,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1e481ae-7f82-4cdf-9c02-0f5d556ced7a/OceanDNA-b24428.fa --refList OceanDNA-b24428/target_genomes.txt --output OceanDNA-b24428/fastani_result.tsv --threads 1
[2023-03-17 15:10:00,420] [INFO] Task succeeded: fastANI
[2023-03-17 15:10:00,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg695b7c6e-e37b-4e1b-9cd7-7fed63e3a853/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 15:10:00,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg695b7c6e-e37b-4e1b-9cd7-7fed63e3a853/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 15:10:00,421] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 15:10:00,421] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 15:10:00,421] [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
--------------------------------------------------------------------------------
[2023-03-17 15:10:00,421] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24428/tc_result.tsv
[2023-03-17 15:10:00,421] [INFO] ===== Taxonomy check completed =====
[2023-03-17 15:10:00,421] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 15:10:00,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg695b7c6e-e37b-4e1b-9cd7-7fed63e3a853/dqc_reference/checkm_data
[2023-03-17 15:10:00,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 15:10:00,426] [INFO] Task started: CheckM
[2023-03-17 15:10:00,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24428/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24428/checkm_input OceanDNA-b24428/checkm_result
[2023-03-17 15:10:17,538] [INFO] Task succeeded: CheckM
[2023-03-17 15:10:17,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.22%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 15:10:17,540] [INFO] ===== Completeness check finished =====
[2023-03-17 15:10:17,540] [INFO] ===== Start GTDB Search =====
[2023-03-17 15:10:17,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24428/markers.fasta)
[2023-03-17 15:10:17,540] [INFO] Task started: Blastn
[2023-03-17 15:10:17,540] [INFO] Running command: blastn -query OceanDNA-b24428/markers.fasta -db /var/lib/cwl/stg695b7c6e-e37b-4e1b-9cd7-7fed63e3a853/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24428/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:10:18,734] [INFO] Task succeeded: Blastn
[2023-03-17 15:10:18,735] [INFO] Selected 24 target genomes.
[2023-03-17 15:10:18,735] [INFO] Target genome list was writen to OceanDNA-b24428/target_genomes_gtdb.txt
[2023-03-17 15:10:19,155] [INFO] Task started: fastANI
[2023-03-17 15:10:19,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1e481ae-7f82-4cdf-9c02-0f5d556ced7a/OceanDNA-b24428.fa --refList OceanDNA-b24428/target_genomes_gtdb.txt --output OceanDNA-b24428/fastani_result_gtdb.tsv --threads 1
[2023-03-17 15:10:27,760] [INFO] Task succeeded: fastANI
[2023-03-17 15:10:27,770] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 15:10:27,770] [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_002938195.1	s__MarineAlpha5-Bin7 sp002938195	77.7751	103	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin7	95.0	99.81	99.67	0.81	0.76	3	-
GCA_902577425.1	s__MarineAlpha5-Bin3 sp902577425	76.9547	77	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	95.54	95.54	0.86	0.86	2	-
GCA_017639935.1	s__JAGFWP01 sp017639935	76.791	74	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__JAGFWP01	95.0	99.64	99.12	0.86	0.76	8	-
GCA_002938205.1	s__AG-337-I02 sp002938205	76.6626	71	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.93	99.93	0.95	0.95	2	-
GCA_902607435.1	s__CACLJX01 sp902607435	76.614	75	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__CACLJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512325.1	s__AG-337-I02 sp902512325	76.497	55	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595425.1	s__AG-337-I02 sp902595425	76.4949	62	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576125.1	s__AG-337-I02 sp902576125	76.4688	54	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560725.1	s__AG-337-I02 sp902560725	76.4379	56	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902561355.1	s__AG-337-I02 sp902561355	76.4166	71	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902553945.1	s__AG-337-I02 sp902553945	76.3807	53	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560675.1	s__AG-337-I02 sp902554185	76.34	51	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	98.99	98.59	0.82	0.79	4	-
GCA_902623255.1	s__AG-337-I02 sp902623255	76.1818	57	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902585605.1	s__AG-337-I02 sp902585605	76.1812	56	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635455.1	s__CACPNW01 sp902635455	76.1805	62	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__CACPNW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902570155.1	s__AG-337-I02 sp902570155	76.1563	55	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	98.44	98.44	0.82	0.82	2	-
GCA_902567135.1	s__AG-337-I02 sp902567135	76.1304	50	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282155.1	s__AG-337-I02 sp003282155	76.1262	55	247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 15:10:27,770] [INFO] GTDB search result was written to OceanDNA-b24428/result_gtdb.tsv
[2023-03-17 15:10:27,770] [INFO] ===== GTDB Search completed =====
[2023-03-17 15:10:27,772] [INFO] DFAST_QC result json was written to OceanDNA-b24428/dqc_result.json
[2023-03-17 15:10:27,772] [INFO] DFAST_QC completed!
[2023-03-17 15:10:27,772] [INFO] Total running time: 0h0m47s