[2023-03-18 20:59:43,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,924] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e9b6c65-0f39-4d50-8b66-24c2d8eb99d5/dqc_reference
[2023-03-18 20:59:45,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,684] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,684] [INFO] Running command: cat /var/lib/cwl/stg7f3a1f9b-3066-4594-94ae-ec42f1d49cf1/OceanDNA-b22652.fa | prodigal -d OceanDNA-b22652/cds.fna -a OceanDNA-b22652/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:55,584] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:55,584] [INFO] Task started: HMMsearch
[2023-03-18 20:59:55,584] [INFO] Running command: hmmsearch --tblout OceanDNA-b22652/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e9b6c65-0f39-4d50-8b66-24c2d8eb99d5/dqc_reference/reference_markers.hmm OceanDNA-b22652/protein.faa > /dev/null
[2023-03-18 20:59:55,790] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:55,791] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7f3a1f9b-3066-4594-94ae-ec42f1d49cf1/OceanDNA-b22652.fa]
[2023-03-18 20:59:55,813] [INFO] Query marker FASTA was written to OceanDNA-b22652/markers.fasta
[2023-03-18 20:59:55,814] [INFO] Task started: Blastn
[2023-03-18 20:59:55,814] [INFO] Running command: blastn -query OceanDNA-b22652/markers.fasta -db /var/lib/cwl/stg8e9b6c65-0f39-4d50-8b66-24c2d8eb99d5/dqc_reference/reference_markers.fasta -out OceanDNA-b22652/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:56,357] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:56,358] [INFO] Selected 20 target genomes.
[2023-03-18 20:59:56,358] [INFO] Target genome list was writen to OceanDNA-b22652/target_genomes.txt
[2023-03-18 20:59:56,374] [INFO] Task started: fastANI
[2023-03-18 20:59:56,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3a1f9b-3066-4594-94ae-ec42f1d49cf1/OceanDNA-b22652.fa --refList OceanDNA-b22652/target_genomes.txt --output OceanDNA-b22652/fastani_result.tsv --threads 1
[2023-03-18 21:00:17,155] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:17,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e9b6c65-0f39-4d50-8b66-24c2d8eb99d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:17,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e9b6c65-0f39-4d50-8b66-24c2d8eb99d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:17,159] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:17,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:00:17,160] [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
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.0521	51	463	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.0006	55	463	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:00:17,160] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22652/tc_result.tsv
[2023-03-18 21:00:17,160] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:17,160] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:17,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e9b6c65-0f39-4d50-8b66-24c2d8eb99d5/dqc_reference/checkm_data
[2023-03-18 21:00:17,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:17,164] [INFO] Task started: CheckM
[2023-03-18 21:00:17,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22652/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22652/checkm_input OceanDNA-b22652/checkm_result
[2023-03-18 21:00:46,326] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:46,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:46,350] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:46,350] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:46,350] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22652/markers.fasta)
[2023-03-18 21:00:46,351] [INFO] Task started: Blastn
[2023-03-18 21:00:46,351] [INFO] Running command: blastn -query OceanDNA-b22652/markers.fasta -db /var/lib/cwl/stg8e9b6c65-0f39-4d50-8b66-24c2d8eb99d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22652/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:47,180] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:47,186] [INFO] Selected 22 target genomes.
[2023-03-18 21:00:47,186] [INFO] Target genome list was writen to OceanDNA-b22652/target_genomes_gtdb.txt
[2023-03-18 21:00:47,208] [INFO] Task started: fastANI
[2023-03-18 21:00:47,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3a1f9b-3066-4594-94ae-ec42f1d49cf1/OceanDNA-b22652.fa --refList OceanDNA-b22652/target_genomes_gtdb.txt --output OceanDNA-b22652/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:01,072] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:01,082] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:01:01,082] [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_009922585.1	s__UBA1268 sp009922585	79.9118	214	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523305.1	s__UBA1268 sp011523305	78.8058	230	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	77.9212	145	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	77.8973	117	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872955.1	s__QWPN01 sp016872955	77.8325	107	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401745.1	s__M30B53 sp018401745	77.7124	106	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__M30B53	95.0	96.02	95.94	0.68	0.66	3	-
GCA_002405515.1	s__UBA4655 sp002405515	77.685	125	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA4655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670825.1	s__QWPN01 sp003670825	77.5372	72	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	77.5075	145	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	77.4551	129	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027105.1	s__RGVT01 sp010027105	77.384	107	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669255.1	s__QWPN01 sp003669255	77.2707	84	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970785.1	s__F1-20-MAGs016 sp018970785	77.1805	98	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903949225.1	s__QWOP01 sp903949225	77.1629	97	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853835.1	s__QWPN01 sp017853835	77.0085	116	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	76.9612	106	463	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:01,082] [INFO] GTDB search result was written to OceanDNA-b22652/result_gtdb.tsv
[2023-03-18 21:01:01,083] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:01,084] [INFO] DFAST_QC result json was written to OceanDNA-b22652/dqc_result.json
[2023-03-18 21:01:01,084] [INFO] DFAST_QC completed!
[2023-03-18 21:01:01,084] [INFO] Total running time: 0h1m17s