[2023-03-16 07:28:29,971] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:29,971] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:29,971] [INFO] DQC Reference Directory: /var/lib/cwl/stged013125-5e03-4eeb-839b-9c2c73267465/dqc_reference
[2023-03-16 07:28:31,056] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,057] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,057] [INFO] Running command: cat /var/lib/cwl/stga270b77e-d0d9-4957-b894-7cd938902b6c/OceanDNA-b45989.fa | prodigal -d OceanDNA-b45989/cds.fna -a OceanDNA-b45989/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:47,322] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:47,322] [INFO] Task started: HMMsearch
[2023-03-16 07:28:47,322] [INFO] Running command: hmmsearch --tblout OceanDNA-b45989/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged013125-5e03-4eeb-839b-9c2c73267465/dqc_reference/reference_markers.hmm OceanDNA-b45989/protein.faa > /dev/null
[2023-03-16 07:28:47,502] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:47,503] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga270b77e-d0d9-4957-b894-7cd938902b6c/OceanDNA-b45989.fa]
[2023-03-16 07:28:47,523] [INFO] Query marker FASTA was written to OceanDNA-b45989/markers.fasta
[2023-03-16 07:28:47,524] [INFO] Task started: Blastn
[2023-03-16 07:28:47,524] [INFO] Running command: blastn -query OceanDNA-b45989/markers.fasta -db /var/lib/cwl/stged013125-5e03-4eeb-839b-9c2c73267465/dqc_reference/reference_markers.fasta -out OceanDNA-b45989/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:48,114] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:48,115] [INFO] Selected 19 target genomes.
[2023-03-16 07:28:48,116] [INFO] Target genome list was writen to OceanDNA-b45989/target_genomes.txt
[2023-03-16 07:28:48,131] [INFO] Task started: fastANI
[2023-03-16 07:28:48,131] [INFO] Running command: fastANI --query /var/lib/cwl/stga270b77e-d0d9-4957-b894-7cd938902b6c/OceanDNA-b45989.fa --refList OceanDNA-b45989/target_genomes.txt --output OceanDNA-b45989/fastani_result.tsv --threads 1
[2023-03-16 07:29:01,083] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:01,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged013125-5e03-4eeb-839b-9c2c73267465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:01,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged013125-5e03-4eeb-839b-9c2c73267465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:01,087] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:01,087] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:29:01,087] [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
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.4634	61	641	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:29:01,088] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45989/tc_result.tsv
[2023-03-16 07:29:01,088] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:01,089] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:01,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged013125-5e03-4eeb-839b-9c2c73267465/dqc_reference/checkm_data
[2023-03-16 07:29:01,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:01,098] [INFO] Task started: CheckM
[2023-03-16 07:29:01,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45989/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45989/checkm_input OceanDNA-b45989/checkm_result
[2023-03-16 07:29:45,344] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:45,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:45,349] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:45,349] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:45,350] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45989/markers.fasta)
[2023-03-16 07:29:45,351] [INFO] Task started: Blastn
[2023-03-16 07:29:45,351] [INFO] Running command: blastn -query OceanDNA-b45989/markers.fasta -db /var/lib/cwl/stged013125-5e03-4eeb-839b-9c2c73267465/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45989/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:46,341] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:46,425] [INFO] Selected 8 target genomes.
[2023-03-16 07:29:46,426] [INFO] Target genome list was writen to OceanDNA-b45989/target_genomes_gtdb.txt
[2023-03-16 07:29:46,598] [INFO] Task started: fastANI
[2023-03-16 07:29:46,598] [INFO] Running command: fastANI --query /var/lib/cwl/stga270b77e-d0d9-4957-b894-7cd938902b6c/OceanDNA-b45989.fa --refList OceanDNA-b45989/target_genomes_gtdb.txt --output OceanDNA-b45989/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:29:50,923] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:50,929] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:29:50,929] [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	93.2531	408	641	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_017854655.1	s__BACL24 sp017854655	88.696	466	641	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_002430605.1	s__BACL24 sp002430605	88.1544	493	641	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_018663485.1	s__BACL24 sp018663485	88.0142	433	641	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	86.7411	460	641	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.51	99.36	0.91	0.87	10	-
GCA_905479975.1	s__BACL24 sp905479975	80.5339	367	641	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902728235.1	s__BACL24 sp902728235	79.957	360	641	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	77.6698	132	641	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.81	99.81	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:29:50,930] [INFO] GTDB search result was written to OceanDNA-b45989/result_gtdb.tsv
[2023-03-16 07:29:50,930] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:29:50,931] [INFO] DFAST_QC result json was written to OceanDNA-b45989/dqc_result.json
[2023-03-16 07:29:50,931] [INFO] DFAST_QC completed!
[2023-03-16 07:29:50,931] [INFO] Total running time: 0h1m21s