[2023-03-16 11:50:51,396] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:50:51,396] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:50:51,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d6fc26c-094a-4124-8c86-f26f39aca517/dqc_reference
[2023-03-16 11:50:54,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:50:54,281] [INFO] Task started: Prodigal
[2023-03-16 11:50:54,281] [INFO] Running command: cat /var/lib/cwl/stg48c2fb6c-7aa7-47fa-92b2-a73ad1857e39/OceanDNA-b22239.fa | prodigal -d OceanDNA-b22239/cds.fna -a OceanDNA-b22239/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:51:11,863] [INFO] Task succeeded: Prodigal
[2023-03-16 11:51:11,863] [INFO] Task started: HMMsearch
[2023-03-16 11:51:11,863] [INFO] Running command: hmmsearch --tblout OceanDNA-b22239/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d6fc26c-094a-4124-8c86-f26f39aca517/dqc_reference/reference_markers.hmm OceanDNA-b22239/protein.faa > /dev/null
[2023-03-16 11:51:12,066] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:51:12,066] [INFO] Found 6/6 markers.
[2023-03-16 11:51:12,088] [INFO] Query marker FASTA was written to OceanDNA-b22239/markers.fasta
[2023-03-16 11:51:12,089] [INFO] Task started: Blastn
[2023-03-16 11:51:12,089] [INFO] Running command: blastn -query OceanDNA-b22239/markers.fasta -db /var/lib/cwl/stg4d6fc26c-094a-4124-8c86-f26f39aca517/dqc_reference/reference_markers.fasta -out OceanDNA-b22239/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:51:12,626] [INFO] Task succeeded: Blastn
[2023-03-16 11:51:12,627] [INFO] Selected 27 target genomes.
[2023-03-16 11:51:12,628] [INFO] Target genome list was writen to OceanDNA-b22239/target_genomes.txt
[2023-03-16 11:51:12,642] [INFO] Task started: fastANI
[2023-03-16 11:51:12,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg48c2fb6c-7aa7-47fa-92b2-a73ad1857e39/OceanDNA-b22239.fa --refList OceanDNA-b22239/target_genomes.txt --output OceanDNA-b22239/fastani_result.tsv --threads 1
[2023-03-16 11:51:38,483] [INFO] Task succeeded: fastANI
[2023-03-16 11:51:38,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d6fc26c-094a-4124-8c86-f26f39aca517/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:51:38,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d6fc26c-094a-4124-8c86-f26f39aca517/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:51:38,484] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:51:38,484] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 11:51:38,484] [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 11:51:38,484] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22239/tc_result.tsv
[2023-03-16 11:51:38,484] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:51:38,485] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:51:38,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d6fc26c-094a-4124-8c86-f26f39aca517/dqc_reference/checkm_data
[2023-03-16 11:51:38,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:51:38,492] [INFO] Task started: CheckM
[2023-03-16 11:51:38,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22239/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22239/checkm_input OceanDNA-b22239/checkm_result
[2023-03-16 11:52:30,518] [INFO] Task succeeded: CheckM
[2023-03-16 11:52:30,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:52:30,521] [INFO] ===== Completeness check finished =====
[2023-03-16 11:52:30,521] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:52:30,522] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22239/markers.fasta)
[2023-03-16 11:52:30,523] [INFO] Task started: Blastn
[2023-03-16 11:52:30,523] [INFO] Running command: blastn -query OceanDNA-b22239/markers.fasta -db /var/lib/cwl/stg4d6fc26c-094a-4124-8c86-f26f39aca517/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22239/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:52:31,337] [INFO] Task succeeded: Blastn
[2023-03-16 11:52:31,337] [INFO] Selected 16 target genomes.
[2023-03-16 11:52:31,337] [INFO] Target genome list was writen to OceanDNA-b22239/target_genomes_gtdb.txt
[2023-03-16 11:52:31,860] [INFO] Task started: fastANI
[2023-03-16 11:52:31,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg48c2fb6c-7aa7-47fa-92b2-a73ad1857e39/OceanDNA-b22239.fa --refList OceanDNA-b22239/target_genomes_gtdb.txt --output OceanDNA-b22239/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:52:41,225] [INFO] Task succeeded: fastANI
[2023-03-16 11:52:41,234] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:52:41,234] [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_002337545.1	s__UBA1924 sp002337545	98.6605	678	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	98.57	98.49	0.90	0.89	3	conclusive
GCA_017642965.1	s__UBA1924 sp017642965	81.818	479	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	80.7496	395	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_003696675.1	s__UBA6054 sp003696675	77.3531	104	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640485.1	s__UBA1924 sp017640485	77.0213	109	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	76.9254	114	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487555.1	s__UBA1924 sp015487555	76.8177	139	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706885.1	s__GCA-2706885 sp002706885	76.6054	51	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2706885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764015.1	s__UBA1924 sp016764015	76.5066	83	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480345.1	s__UBA1926 sp002480345	76.5029	84	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401225.1	s__UBA1924 sp002401225	76.3812	55	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	76.0798	52	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007124345.1	s__SLFH01 sp007124345	75.6773	50	727	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-16 11:52:41,234] [INFO] GTDB search result was written to OceanDNA-b22239/result_gtdb.tsv
[2023-03-16 11:52:41,234] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:52:41,235] [INFO] DFAST_QC result json was written to OceanDNA-b22239/dqc_result.json
[2023-03-16 11:52:41,236] [INFO] DFAST_QC completed!
[2023-03-16 11:52:41,236] [INFO] Total running time: 0h1m50s