[2023-03-18 07:29:30,339] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,339] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg82fd783e-9e6c-4b11-903c-a94ce4386b3d/dqc_reference
[2023-03-18 07:29:31,936] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,937] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,937] [INFO] Running command: cat /var/lib/cwl/stg5498dc95-1885-4078-b841-58adf2c9f876/OceanDNA-b46010.fa | prodigal -d OceanDNA-b46010/cds.fna -a OceanDNA-b46010/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:46,816] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:46,816] [INFO] Task started: HMMsearch
[2023-03-18 07:29:46,816] [INFO] Running command: hmmsearch --tblout OceanDNA-b46010/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82fd783e-9e6c-4b11-903c-a94ce4386b3d/dqc_reference/reference_markers.hmm OceanDNA-b46010/protein.faa > /dev/null
[2023-03-18 07:29:46,975] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:46,975] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5498dc95-1885-4078-b841-58adf2c9f876/OceanDNA-b46010.fa]
[2023-03-18 07:29:46,990] [INFO] Query marker FASTA was written to OceanDNA-b46010/markers.fasta
[2023-03-18 07:29:46,990] [INFO] Task started: Blastn
[2023-03-18 07:29:46,990] [INFO] Running command: blastn -query OceanDNA-b46010/markers.fasta -db /var/lib/cwl/stg82fd783e-9e6c-4b11-903c-a94ce4386b3d/dqc_reference/reference_markers.fasta -out OceanDNA-b46010/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:47,503] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:47,504] [INFO] Selected 17 target genomes.
[2023-03-18 07:29:47,504] [INFO] Target genome list was writen to OceanDNA-b46010/target_genomes.txt
[2023-03-18 07:29:47,514] [INFO] Task started: fastANI
[2023-03-18 07:29:47,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg5498dc95-1885-4078-b841-58adf2c9f876/OceanDNA-b46010.fa --refList OceanDNA-b46010/target_genomes.txt --output OceanDNA-b46010/fastani_result.tsv --threads 1
[2023-03-18 07:29:57,865] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:57,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82fd783e-9e6c-4b11-903c-a94ce4386b3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:57,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82fd783e-9e6c-4b11-903c-a94ce4386b3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:57,865] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:57,865] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:57,865] [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 07:29:57,866] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46010/tc_result.tsv
[2023-03-18 07:29:57,866] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:57,866] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:57,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82fd783e-9e6c-4b11-903c-a94ce4386b3d/dqc_reference/checkm_data
[2023-03-18 07:29:57,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:57,872] [INFO] Task started: CheckM
[2023-03-18 07:29:57,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46010/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46010/checkm_input OceanDNA-b46010/checkm_result
[2023-03-18 07:30:39,348] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:39,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:39,350] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:39,350] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:39,350] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46010/markers.fasta)
[2023-03-18 07:30:39,350] [INFO] Task started: Blastn
[2023-03-18 07:30:39,351] [INFO] Running command: blastn -query OceanDNA-b46010/markers.fasta -db /var/lib/cwl/stg82fd783e-9e6c-4b11-903c-a94ce4386b3d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46010/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:40,100] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:40,101] [INFO] Selected 9 target genomes.
[2023-03-18 07:30:40,101] [INFO] Target genome list was writen to OceanDNA-b46010/target_genomes_gtdb.txt
[2023-03-18 07:30:40,273] [INFO] Task started: fastANI
[2023-03-18 07:30:40,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg5498dc95-1885-4078-b841-58adf2c9f876/OceanDNA-b46010.fa --refList OceanDNA-b46010/target_genomes_gtdb.txt --output OceanDNA-b46010/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:44,645] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:44,650] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:44,651] [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_905182435.1	s__BACL24 sp905182435	81.7661	288	563	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430605.1	s__BACL24 sp002430605	81.5726	343	563	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.69	99.69	0.90	0.90	2	-
GCA_017854655.1	s__BACL24 sp017854655	81.2584	307	563	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.39	99.26	0.93	0.92	3	-
GCA_018663485.1	s__BACL24 sp018663485	80.5725	291	563	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479975.1	s__BACL24 sp905479975	80.4774	323	563	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292345.1	s__BACL24 sp002292345	80.4008	280	563	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.51	99.36	0.91	0.87	10	-
GCF_902728235.1	s__BACL24 sp902728235	79.5413	304	563	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.30	98.39	0.95	0.90	8	-
GCA_018607135.1	s__BACL24 sp003485085	76.8757	104	563	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.81	99.81	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:44,651] [INFO] GTDB search result was written to OceanDNA-b46010/result_gtdb.tsv
[2023-03-18 07:30:44,651] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:44,652] [INFO] DFAST_QC result json was written to OceanDNA-b46010/dqc_result.json
[2023-03-18 07:30:44,652] [INFO] DFAST_QC completed!
[2023-03-18 07:30:44,652] [INFO] Total running time: 0h1m14s