[2023-03-16 04:05:20,067] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,067] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,067] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b0e62f2-3873-4162-9008-61d4a5bb344b/dqc_reference
[2023-03-16 04:05:21,149] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:21,149] [INFO] Task started: Prodigal
[2023-03-16 04:05:21,149] [INFO] Running command: cat /var/lib/cwl/stg38ce2edc-e7ac-429b-a341-6160b51ff150/OceanDNA-b5282.fa | prodigal -d OceanDNA-b5282/cds.fna -a OceanDNA-b5282/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:36,525] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:36,525] [INFO] Task started: HMMsearch
[2023-03-16 04:05:36,525] [INFO] Running command: hmmsearch --tblout OceanDNA-b5282/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b0e62f2-3873-4162-9008-61d4a5bb344b/dqc_reference/reference_markers.hmm OceanDNA-b5282/protein.faa > /dev/null
[2023-03-16 04:05:36,712] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:36,713] [INFO] Found 6/6 markers.
[2023-03-16 04:05:36,727] [INFO] Query marker FASTA was written to OceanDNA-b5282/markers.fasta
[2023-03-16 04:05:36,728] [INFO] Task started: Blastn
[2023-03-16 04:05:36,728] [INFO] Running command: blastn -query OceanDNA-b5282/markers.fasta -db /var/lib/cwl/stg0b0e62f2-3873-4162-9008-61d4a5bb344b/dqc_reference/reference_markers.fasta -out OceanDNA-b5282/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:37,271] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:37,272] [INFO] Selected 31 target genomes.
[2023-03-16 04:05:37,272] [INFO] Target genome list was writen to OceanDNA-b5282/target_genomes.txt
[2023-03-16 04:05:37,286] [INFO] Task started: fastANI
[2023-03-16 04:05:37,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg38ce2edc-e7ac-429b-a341-6160b51ff150/OceanDNA-b5282.fa --refList OceanDNA-b5282/target_genomes.txt --output OceanDNA-b5282/fastani_result.tsv --threads 1
[2023-03-16 04:05:53,920] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:53,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b0e62f2-3873-4162-9008-61d4a5bb344b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:53,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b0e62f2-3873-4162-9008-61d4a5bb344b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:53,926] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:53,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:05:53,926] [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
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	75.8304	50	852	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	75.6305	54	852	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	75.6079	55	852	95	below_threshold
Brumimicrobium aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	75.3936	51	852	95	below_threshold
Vicingus serpentipes	strain=NCIMB 15042	GCA_007993035.1	1926625	1926625	type	True	75.2435	50	852	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.1321	51	852	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:05:53,926] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5282/tc_result.tsv
[2023-03-16 04:05:53,926] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:53,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:53,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b0e62f2-3873-4162-9008-61d4a5bb344b/dqc_reference/checkm_data
[2023-03-16 04:05:53,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:53,931] [INFO] Task started: CheckM
[2023-03-16 04:05:53,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5282/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5282/checkm_input OceanDNA-b5282/checkm_result
[2023-03-16 04:06:34,674] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:34,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:34,677] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:34,677] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:34,677] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5282/markers.fasta)
[2023-03-16 04:06:34,677] [INFO] Task started: Blastn
[2023-03-16 04:06:34,677] [INFO] Running command: blastn -query OceanDNA-b5282/markers.fasta -db /var/lib/cwl/stg0b0e62f2-3873-4162-9008-61d4a5bb344b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5282/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:35,435] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:35,436] [INFO] Selected 22 target genomes.
[2023-03-16 04:06:35,436] [INFO] Target genome list was writen to OceanDNA-b5282/target_genomes_gtdb.txt
[2023-03-16 04:06:35,477] [INFO] Task started: fastANI
[2023-03-16 04:06:35,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg38ce2edc-e7ac-429b-a341-6160b51ff150/OceanDNA-b5282.fa --refList OceanDNA-b5282/target_genomes_gtdb.txt --output OceanDNA-b5282/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:46,240] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:46,245] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:06:46,245] [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_016178305.1	s__CAIUKX01 sp016178305	77.0174	151	852	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903899795.1	s__CAIUKX01 sp903899795	76.764	93	852	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885545.1	s__M0103 sp009885545	76.4447	85	852	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945495.1	s__M0103 sp903945495	76.3938	95	852	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
GCA_017984635.1	s__M0103 sp017984635	76.1095	90	852	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983675.1	s__Fluviicola sp017983675	75.9416	60	852	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	99.86	99.86	0.97	0.97	2	-
GCA_018883325.1	s__UBA952 sp018883325	75.8698	69	852	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183815.1	s__M2408 sp016183815	75.6932	62	852	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M2408	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:46,245] [INFO] GTDB search result was written to OceanDNA-b5282/result_gtdb.tsv
[2023-03-16 04:06:46,245] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:46,246] [INFO] DFAST_QC result json was written to OceanDNA-b5282/dqc_result.json
[2023-03-16 04:06:46,246] [INFO] DFAST_QC completed!
[2023-03-16 04:06:46,247] [INFO] Total running time: 0h1m26s