[2023-03-17 11:52:51,152] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:52:51,154] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:52:51,154] [INFO] DQC Reference Directory: /var/lib/cwl/stge4184a30-820e-4525-acaf-e5a41e52da9f/dqc_reference
[2023-03-17 11:52:52,827] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:52:52,828] [INFO] Task started: Prodigal
[2023-03-17 11:52:52,828] [INFO] Running command: cat /var/lib/cwl/stgae890187-cf7a-4709-bb90-25660c9e7357/OceanDNA-b30213.fa | prodigal -d OceanDNA-b30213/cds.fna -a OceanDNA-b30213/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:53:15,243] [INFO] Task succeeded: Prodigal
[2023-03-17 11:53:15,244] [INFO] Task started: HMMsearch
[2023-03-17 11:53:15,244] [INFO] Running command: hmmsearch --tblout OceanDNA-b30213/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4184a30-820e-4525-acaf-e5a41e52da9f/dqc_reference/reference_markers.hmm OceanDNA-b30213/protein.faa > /dev/null
[2023-03-17 11:53:15,443] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:53:15,443] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgae890187-cf7a-4709-bb90-25660c9e7357/OceanDNA-b30213.fa]
[2023-03-17 11:53:15,506] [INFO] Query marker FASTA was written to OceanDNA-b30213/markers.fasta
[2023-03-17 11:53:15,507] [INFO] Task started: Blastn
[2023-03-17 11:53:15,507] [INFO] Running command: blastn -query OceanDNA-b30213/markers.fasta -db /var/lib/cwl/stge4184a30-820e-4525-acaf-e5a41e52da9f/dqc_reference/reference_markers.fasta -out OceanDNA-b30213/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:53:16,293] [INFO] Task succeeded: Blastn
[2023-03-17 11:53:16,308] [INFO] Selected 22 target genomes.
[2023-03-17 11:53:16,308] [INFO] Target genome list was writen to OceanDNA-b30213/target_genomes.txt
[2023-03-17 11:53:16,320] [INFO] Task started: fastANI
[2023-03-17 11:53:16,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgae890187-cf7a-4709-bb90-25660c9e7357/OceanDNA-b30213.fa --refList OceanDNA-b30213/target_genomes.txt --output OceanDNA-b30213/fastani_result.tsv --threads 1
[2023-03-17 11:53:31,775] [INFO] Task succeeded: fastANI
[2023-03-17 11:53:31,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4184a30-820e-4525-acaf-e5a41e52da9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:53:31,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4184a30-820e-4525-acaf-e5a41e52da9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:53:31,789] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:53:31,789] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:53:31,789] [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
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	79.1086	529	1150	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	78.5551	440	1150	95	below_threshold
Sulfitobacter guttiformis	strain=DSM 11458	GCA_003610455.1	74349	74349	type	True	78.5457	495	1150	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.2295	470	1150	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.2247	475	1150	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.197	458	1150	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.0272	356	1150	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.0227	362	1150	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.8393	390	1150	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	77.7144	333	1150	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.6685	332	1150	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.6313	329	1150	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.4277	327	1150	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.3794	344	1150	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.3014	380	1150	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.2062	305	1150	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.1812	295	1150	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.1259	218	1150	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.1255	218	1150	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.0404	209	1150	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	76.9496	209	1150	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.7421	232	1150	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:53:31,797] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30213/tc_result.tsv
[2023-03-17 11:53:31,810] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:53:31,810] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:53:31,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4184a30-820e-4525-acaf-e5a41e52da9f/dqc_reference/checkm_data
[2023-03-17 11:53:31,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:53:31,823] [INFO] Task started: CheckM
[2023-03-17 11:53:31,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30213/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30213/checkm_input OceanDNA-b30213/checkm_result
[2023-03-17 11:54:28,092] [INFO] Task succeeded: CheckM
[2023-03-17 11:54:28,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:54:28,396] [INFO] ===== Completeness check finished =====
[2023-03-17 11:54:28,396] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:54:28,397] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30213/markers.fasta)
[2023-03-17 11:54:28,398] [INFO] Task started: Blastn
[2023-03-17 11:54:28,398] [INFO] Running command: blastn -query OceanDNA-b30213/markers.fasta -db /var/lib/cwl/stge4184a30-820e-4525-acaf-e5a41e52da9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30213/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:54:29,828] [INFO] Task succeeded: Blastn
[2023-03-17 11:54:29,851] [INFO] Selected 20 target genomes.
[2023-03-17 11:54:29,851] [INFO] Target genome list was writen to OceanDNA-b30213/target_genomes_gtdb.txt
[2023-03-17 11:54:29,894] [INFO] Task started: fastANI
[2023-03-17 11:54:29,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgae890187-cf7a-4709-bb90-25660c9e7357/OceanDNA-b30213.fa --refList OceanDNA-b30213/target_genomes_gtdb.txt --output OceanDNA-b30213/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:54:45,028] [INFO] Task succeeded: fastANI
[2023-03-17 11:54:45,039] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:54:45,039] [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
GCF_018200035.1	s__Sulfitobacter sp018200035	79.1309	628	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196805.1	s__Sulfitobacter undariae	79.0913	531	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	78.5551	440	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003610455.1	s__Sulfitobacter guttiformis	78.5457	495	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001650875.1	s__Sulfitobacter sp001650875	78.5015	512	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.4077	485	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	78.3731	420	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.2053	473	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCA_017854855.1	s__Sulfitobacter sp017854855	78.2	418	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172095.1	s__Sulfitobacter indolifex	78.0272	356	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112755.1	s__Sulfitobacter brevis	77.8887	394	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.8393	390	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	77.7417	370	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	77.6685	332	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116285.1	s__Sulfitobacter marinus	77.6223	330	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.6025	401	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.3794	344	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013317235.1	s__Leisingera sp013317235	77.3388	337	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.2944	381	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.2079	304	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:54:45,044] [INFO] GTDB search result was written to OceanDNA-b30213/result_gtdb.tsv
[2023-03-17 11:54:45,048] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:54:45,054] [INFO] DFAST_QC result json was written to OceanDNA-b30213/dqc_result.json
[2023-03-17 11:54:45,054] [INFO] DFAST_QC completed!
[2023-03-17 11:54:45,055] [INFO] Total running time: 0h1m54s