[2023-03-17 11:00:12,903] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:00:12,904] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:00:12,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg99e451aa-1c6f-4c9d-8a50-6bcfc46b080c/dqc_reference
[2023-03-17 11:00:14,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:00:14,075] [INFO] Task started: Prodigal
[2023-03-17 11:00:14,075] [INFO] Running command: cat /var/lib/cwl/stg255fabef-1c5e-473a-82d6-929f33167170/OceanDNA-b42816.fa | prodigal -d OceanDNA-b42816/cds.fna -a OceanDNA-b42816/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:00:29,047] [INFO] Task succeeded: Prodigal
[2023-03-17 11:00:29,047] [INFO] Task started: HMMsearch
[2023-03-17 11:00:29,047] [INFO] Running command: hmmsearch --tblout OceanDNA-b42816/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99e451aa-1c6f-4c9d-8a50-6bcfc46b080c/dqc_reference/reference_markers.hmm OceanDNA-b42816/protein.faa > /dev/null
[2023-03-17 11:00:29,223] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:00:29,223] [INFO] Found 6/6 markers.
[2023-03-17 11:00:29,238] [INFO] Query marker FASTA was written to OceanDNA-b42816/markers.fasta
[2023-03-17 11:00:29,239] [INFO] Task started: Blastn
[2023-03-17 11:00:29,239] [INFO] Running command: blastn -query OceanDNA-b42816/markers.fasta -db /var/lib/cwl/stg99e451aa-1c6f-4c9d-8a50-6bcfc46b080c/dqc_reference/reference_markers.fasta -out OceanDNA-b42816/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:00:29,969] [INFO] Task succeeded: Blastn
[2023-03-17 11:00:29,970] [INFO] Selected 32 target genomes.
[2023-03-17 11:00:29,971] [INFO] Target genome list was writen to OceanDNA-b42816/target_genomes.txt
[2023-03-17 11:00:30,198] [INFO] Task started: fastANI
[2023-03-17 11:00:30,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg255fabef-1c5e-473a-82d6-929f33167170/OceanDNA-b42816.fa --refList OceanDNA-b42816/target_genomes.txt --output OceanDNA-b42816/fastani_result.tsv --threads 1
[2023-03-17 11:00:51,205] [INFO] Task succeeded: fastANI
[2023-03-17 11:00:51,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99e451aa-1c6f-4c9d-8a50-6bcfc46b080c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:00:51,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99e451aa-1c6f-4c9d-8a50-6bcfc46b080c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:00:51,220] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:00:51,220] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:00:51,221] [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
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	77.0324	129	785	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.9737	130	785	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.7758	131	785	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.7459	119	785	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.7344	129	785	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	76.7281	107	785	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.5798	106	785	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.5678	108	785	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.5361	74	785	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.4971	106	785	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.4566	120	785	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	76.4519	66	785	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.4378	116	785	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	76.3937	70	785	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	76.3654	83	785	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.3635	83	785	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.0959	98	785	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.0869	68	785	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	76.0612	97	785	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.0425	79	785	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	75.9631	59	785	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	75.9492	52	785	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.8843	108	785	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.8383	86	785	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.8164	101	785	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.7513	57	785	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.7273	97	785	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:00:51,221] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42816/tc_result.tsv
[2023-03-17 11:00:51,221] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:00:51,221] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:00:51,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99e451aa-1c6f-4c9d-8a50-6bcfc46b080c/dqc_reference/checkm_data
[2023-03-17 11:00:51,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:00:51,395] [INFO] Task started: CheckM
[2023-03-17 11:00:51,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42816/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42816/checkm_input OceanDNA-b42816/checkm_result
[2023-03-17 11:01:32,480] [INFO] Task succeeded: CheckM
[2023-03-17 11:01:32,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:01:32,488] [INFO] ===== Completeness check finished =====
[2023-03-17 11:01:32,488] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:01:32,488] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42816/markers.fasta)
[2023-03-17 11:01:32,489] [INFO] Task started: Blastn
[2023-03-17 11:01:32,489] [INFO] Running command: blastn -query OceanDNA-b42816/markers.fasta -db /var/lib/cwl/stg99e451aa-1c6f-4c9d-8a50-6bcfc46b080c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42816/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:01:33,886] [INFO] Task succeeded: Blastn
[2023-03-17 11:01:33,889] [INFO] Selected 14 target genomes.
[2023-03-17 11:01:33,889] [INFO] Target genome list was writen to OceanDNA-b42816/target_genomes_gtdb.txt
[2023-03-17 11:01:33,897] [INFO] Task started: fastANI
[2023-03-17 11:01:33,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg255fabef-1c5e-473a-82d6-929f33167170/OceanDNA-b42816.fa --refList OceanDNA-b42816/target_genomes_gtdb.txt --output OceanDNA-b42816/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:01:41,553] [INFO] Task succeeded: fastANI
[2023-03-17 11:01:41,562] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:01:41,562] [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_002292945.1	s__UBA964 sp002292945	92.2445	592	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.79	98.79	0.90	0.90	2	-
GCA_009923475.1	s__UBA964 sp009923475	82.6905	324	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938365.1	s__UBA964 sp903938365	79.2776	303	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.27	99.13	0.88	0.87	4	-
GCA_903885195.1	s__UBA964 sp903885195	78.9308	267	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.55	99.16	0.90	0.86	6	-
GCA_017853555.1	s__UBA964 sp017853555	78.6583	259	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010029775.1	s__UBA964 sp010029775	78.5234	173	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010031985.1	s__UBA964 sp010031985	78.4481	198	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.93	98.76	0.80	0.76	12	-
GCA_018883185.1	s__UBA964 sp018883185	78.4292	284	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874175.1	s__UBA964 sp016874175	78.2752	207	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903910215.1	s__UBA964 sp903910215	78.0314	147	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.86	98.86	0.82	0.82	2	-
GCA_016874235.1	s__UBA964 sp016874235	77.9913	183	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	95.25	95.25	0.78	0.78	2	-
GCA_002255905.1	s__PBB1 sp002255905	76.0142	71	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PBB1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467315.1	s__OAE585 sp016467315	75.9082	131	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__OAE585	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583785.1	s__Rubrivivax gelatinosus_B	75.8307	128	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.02	99.02	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:01:41,564] [INFO] GTDB search result was written to OceanDNA-b42816/result_gtdb.tsv
[2023-03-17 11:01:41,566] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:01:41,570] [INFO] DFAST_QC result json was written to OceanDNA-b42816/dqc_result.json
[2023-03-17 11:01:41,570] [INFO] DFAST_QC completed!
[2023-03-17 11:01:41,570] [INFO] Total running time: 0h1m29s