[2023-03-18 11:00:46,280] [INFO] DFAST_QC pipeline started.
[2023-03-18 11:00:46,283] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 11:00:46,284] [INFO] DQC Reference Directory: /var/lib/cwl/stge76c262b-948a-4e95-9261-ceba709a10df/dqc_reference
[2023-03-18 11:00:47,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 11:00:47,993] [INFO] Task started: Prodigal
[2023-03-18 11:00:47,993] [INFO] Running command: cat /var/lib/cwl/stg5dc5bb06-98ee-4a04-b817-e5c0840fef54/OceanDNA-b27370.fa | prodigal -d OceanDNA-b27370/cds.fna -a OceanDNA-b27370/protein.faa -g 11 -q > /dev/null
[2023-03-18 11:00:54,264] [INFO] Task succeeded: Prodigal
[2023-03-18 11:00:54,264] [INFO] Task started: HMMsearch
[2023-03-18 11:00:54,264] [INFO] Running command: hmmsearch --tblout OceanDNA-b27370/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge76c262b-948a-4e95-9261-ceba709a10df/dqc_reference/reference_markers.hmm OceanDNA-b27370/protein.faa > /dev/null
[2023-03-18 11:00:54,454] [INFO] Task succeeded: HMMsearch
[2023-03-18 11:00:54,455] [INFO] Found 6/6 markers.
[2023-03-18 11:00:54,470] [INFO] Query marker FASTA was written to OceanDNA-b27370/markers.fasta
[2023-03-18 11:00:54,472] [INFO] Task started: Blastn
[2023-03-18 11:00:54,472] [INFO] Running command: blastn -query OceanDNA-b27370/markers.fasta -db /var/lib/cwl/stge76c262b-948a-4e95-9261-ceba709a10df/dqc_reference/reference_markers.fasta -out OceanDNA-b27370/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 11:00:55,197] [INFO] Task succeeded: Blastn
[2023-03-18 11:00:55,204] [INFO] Selected 20 target genomes.
[2023-03-18 11:00:55,205] [INFO] Target genome list was writen to OceanDNA-b27370/target_genomes.txt
[2023-03-18 11:00:55,275] [INFO] Task started: fastANI
[2023-03-18 11:00:55,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dc5bb06-98ee-4a04-b817-e5c0840fef54/OceanDNA-b27370.fa --refList OceanDNA-b27370/target_genomes.txt --output OceanDNA-b27370/fastani_result.tsv --threads 1
[2023-03-18 11:01:01,348] [INFO] Task succeeded: fastANI
[2023-03-18 11:01:01,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge76c262b-948a-4e95-9261-ceba709a10df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 11:01:01,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge76c262b-948a-4e95-9261-ceba709a10df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 11:01:01,348] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 11:01:01,348] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 11:01:01,348] [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 11:01:01,351] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27370/tc_result.tsv
[2023-03-18 11:01:01,355] [INFO] ===== Taxonomy check completed =====
[2023-03-18 11:01:01,355] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 11:01:01,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge76c262b-948a-4e95-9261-ceba709a10df/dqc_reference/checkm_data
[2023-03-18 11:01:01,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 11:01:01,413] [INFO] Task started: CheckM
[2023-03-18 11:01:01,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27370/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27370/checkm_input OceanDNA-b27370/checkm_result
[2023-03-18 11:01:29,356] [INFO] Task succeeded: CheckM
[2023-03-18 11:01:29,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 9.38%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 11:01:29,410] [INFO] ===== Completeness check finished =====
[2023-03-18 11:01:29,410] [INFO] ===== Start GTDB Search =====
[2023-03-18 11:01:29,411] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27370/markers.fasta)
[2023-03-18 11:01:29,412] [INFO] Task started: Blastn
[2023-03-18 11:01:29,412] [INFO] Running command: blastn -query OceanDNA-b27370/markers.fasta -db /var/lib/cwl/stge76c262b-948a-4e95-9261-ceba709a10df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27370/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 11:01:30,843] [INFO] Task succeeded: Blastn
[2023-03-18 11:01:30,847] [INFO] Selected 10 target genomes.
[2023-03-18 11:01:30,847] [INFO] Target genome list was writen to OceanDNA-b27370/target_genomes_gtdb.txt
[2023-03-18 11:01:30,853] [INFO] Task started: fastANI
[2023-03-18 11:01:30,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dc5bb06-98ee-4a04-b817-e5c0840fef54/OceanDNA-b27370.fa --refList OceanDNA-b27370/target_genomes_gtdb.txt --output OceanDNA-b27370/fastani_result_gtdb.tsv --threads 1
[2023-03-18 11:01:33,376] [INFO] Task succeeded: fastANI
[2023-03-18 11:01:33,382] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 11:01:33,382] [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_002723035.1	s__MED-G09 sp002723035	99.3318	252	391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002683015.1	s__MED-G09 sp002683015	90.1834	208	391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626605.1	s__MED-G09 sp902626605	88.7875	323	391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003279705.1	s__MED-G09 sp003279705	88.7716	256	391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	99.31	98.62	0.86	0.72	3	-
GCA_902537725.1	s__MED-G09 sp902537725	84.3473	226	391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278145.1	s__MED-G09 sp003278145	83.6262	318	391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	98.26	96.25	0.89	0.83	4	-
GCA_002170885.2	s__MED-G09 sp002170885	79.7814	151	391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704345.1	s__MED-G09 sp002704345	77.9164	122	391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	99.20	99.20	0.77	0.77	2	-
GCA_003209955.1	s__AG-430-B22 sp003209955	77.2444	56	391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-18 11:01:33,383] [INFO] GTDB search result was written to OceanDNA-b27370/result_gtdb.tsv
[2023-03-18 11:01:33,384] [INFO] ===== GTDB Search completed =====
[2023-03-18 11:01:33,386] [INFO] DFAST_QC result json was written to OceanDNA-b27370/dqc_result.json
[2023-03-18 11:01:33,386] [INFO] DFAST_QC completed!
[2023-03-18 11:01:33,386] [INFO] Total running time: 0h0m47s