[2023-03-19 03:22:59,805] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:22:59,807] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:22:59,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg06ac5404-ab0b-435a-b138-db184894155e/dqc_reference
[2023-03-19 03:23:00,915] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:23:00,915] [INFO] Task started: Prodigal
[2023-03-19 03:23:00,916] [INFO] Running command: cat /var/lib/cwl/stg6cb2ac5d-8d9e-4cab-83ba-0a8c5c2cc2ab/OceanDNA-b22805.fa | prodigal -d OceanDNA-b22805/cds.fna -a OceanDNA-b22805/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:24:05,419] [INFO] Task succeeded: Prodigal
[2023-03-19 03:24:05,420] [INFO] Task started: HMMsearch
[2023-03-19 03:24:05,420] [INFO] Running command: hmmsearch --tblout OceanDNA-b22805/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06ac5404-ab0b-435a-b138-db184894155e/dqc_reference/reference_markers.hmm OceanDNA-b22805/protein.faa > /dev/null
[2023-03-19 03:24:05,763] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:24:05,764] [INFO] Found 6/6 markers.
[2023-03-19 03:24:05,829] [INFO] Query marker FASTA was written to OceanDNA-b22805/markers.fasta
[2023-03-19 03:24:05,830] [INFO] Task started: Blastn
[2023-03-19 03:24:05,830] [INFO] Running command: blastn -query OceanDNA-b22805/markers.fasta -db /var/lib/cwl/stg06ac5404-ab0b-435a-b138-db184894155e/dqc_reference/reference_markers.fasta -out OceanDNA-b22805/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:24:06,382] [INFO] Task succeeded: Blastn
[2023-03-19 03:24:06,386] [INFO] Selected 29 target genomes.
[2023-03-19 03:24:06,386] [INFO] Target genome list was writen to OceanDNA-b22805/target_genomes.txt
[2023-03-19 03:24:06,403] [INFO] Task started: fastANI
[2023-03-19 03:24:06,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb2ac5d-8d9e-4cab-83ba-0a8c5c2cc2ab/OceanDNA-b22805.fa --refList OceanDNA-b22805/target_genomes.txt --output OceanDNA-b22805/fastani_result.tsv --threads 1
[2023-03-19 03:24:31,223] [INFO] Task succeeded: fastANI
[2023-03-19 03:24:31,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06ac5404-ab0b-435a-b138-db184894155e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:24:31,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06ac5404-ab0b-435a-b138-db184894155e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:24:31,233] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:24:31,233] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:24:31,233] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.333	129	3353	95	below_threshold
Calycomorphotria hydatis	strain=V22	GCA_007745435.1	2528027	2528027	type	True	75.2088	51	3353	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	75.1524	51	3353	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_008298035.1	122	122	type	True	75.1154	54	3353	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_009720545.1	122	122	type	True	75.1134	54	3353	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.0952	51	3353	95	below_threshold
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	75.0365	72	3353	95	below_threshold
Gimesia benthica	strain=E7	GCA_009720525.1	2608982	2608982	type	True	74.919	59	3353	95	below_threshold
Gimesia chilikensis	strain=JC646	GCA_008329715.1	2605989	2605989	type	True	74.9004	60	3353	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8257	62	3353	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	74.7754	62	3353	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.7734	83	3353	95	below_threshold
Roseimaritima ulvae	strain=UC8	GCA_008065135.1	980254	980254	type	True	74.7688	63	3353	95	below_threshold
Tautonia marina	strain=JC650	GCA_009177065.1	2653855	2653855	type	True	74.6532	61	3353	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:24:31,236] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22805/tc_result.tsv
[2023-03-19 03:24:31,239] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:24:31,239] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:24:31,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06ac5404-ab0b-435a-b138-db184894155e/dqc_reference/checkm_data
[2023-03-19 03:24:31,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:24:31,252] [INFO] Task started: CheckM
[2023-03-19 03:24:31,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22805/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22805/checkm_input OceanDNA-b22805/checkm_result
[2023-03-19 03:27:09,704] [INFO] Task succeeded: CheckM
[2023-03-19 03:27:09,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:27:09,759] [INFO] ===== Completeness check finished =====
[2023-03-19 03:27:09,759] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:27:09,759] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22805/markers.fasta)
[2023-03-19 03:27:09,761] [INFO] Task started: Blastn
[2023-03-19 03:27:09,761] [INFO] Running command: blastn -query OceanDNA-b22805/markers.fasta -db /var/lib/cwl/stg06ac5404-ab0b-435a-b138-db184894155e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22805/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:27:10,531] [INFO] Task succeeded: Blastn
[2023-03-19 03:27:10,532] [INFO] Selected 35 target genomes.
[2023-03-19 03:27:10,532] [INFO] Target genome list was writen to OceanDNA-b22805/target_genomes_gtdb.txt
[2023-03-19 03:27:10,617] [INFO] Task started: fastANI
[2023-03-19 03:27:10,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb2ac5d-8d9e-4cab-83ba-0a8c5c2cc2ab/OceanDNA-b22805.fa --refList OceanDNA-b22805/target_genomes_gtdb.txt --output OceanDNA-b22805/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:27:38,514] [INFO] Task succeeded: fastANI
[2023-03-19 03:27:38,523] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:27:38,524] [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_016124895.1	s__JABMPE01 sp016124895	75.9767	338	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699955.1	s__JABISG01 sp018699955	75.5582	126	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABISG01	95.0	99.95	99.95	0.96	0.96	3	-
GCA_017795105.1	s__Rubinisphaera sp017795105	75.3781	82	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.3587	122	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299185.1	s__AM-0621 sp900299185	75.3581	117	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__AM-0621	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669125.1	s__SXKJ01 sp003669125	75.2917	127	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.07	98.94	0.92	0.91	3	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.2365	77	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745435.1	s__Calycomorphotria hydatis	75.2072	51	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Calycomorphotria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485495.1	s__S139-18 sp015485495	75.1939	70	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__S139-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671275.1	s__TH-plancto1 sp003671275	75.173	50	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__TH-plancto1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298035.1	s__Gimesia maris	75.1045	55	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	98.48	97.03	0.94	0.89	7	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	75.0527	118	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCA_016177915.1	s__JACOUI01 sp016177915	74.9936	70	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JACOUI01;g__JACOUI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003508595.1	s__UBA10511 sp003508595	74.9516	70	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__UBA10511	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720525.1	s__Gimesia benthica	74.9255	58	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.18	95.18	0.86	0.86	2	-
GCF_008329715.1	s__Gimesia chilikensis	74.9113	58	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.30	95.11	0.90	0.87	4	-
GCF_008065135.1	s__Roseimaritima ulvae	74.7741	61	3353	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:27:38,524] [INFO] GTDB search result was written to OceanDNA-b22805/result_gtdb.tsv
[2023-03-19 03:27:38,524] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:27:38,526] [INFO] DFAST_QC result json was written to OceanDNA-b22805/dqc_result.json
[2023-03-19 03:27:38,526] [INFO] DFAST_QC completed!
[2023-03-19 03:27:38,526] [INFO] Total running time: 0h4m39s