[2023-03-16 08:15:57,614] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:15:57,614] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:15:57,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc3dbac6-8778-49e3-b28d-8c32978740d2/dqc_reference
[2023-03-16 08:15:58,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:15:58,760] [INFO] Task started: Prodigal
[2023-03-16 08:15:58,761] [INFO] Running command: cat /var/lib/cwl/stg2989b629-3809-4163-bdf0-08a85a1f30cc/OceanDNA-b32783.fa | prodigal -d OceanDNA-b32783/cds.fna -a OceanDNA-b32783/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:16:17,076] [INFO] Task succeeded: Prodigal
[2023-03-16 08:16:17,076] [INFO] Task started: HMMsearch
[2023-03-16 08:16:17,076] [INFO] Running command: hmmsearch --tblout OceanDNA-b32783/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc3dbac6-8778-49e3-b28d-8c32978740d2/dqc_reference/reference_markers.hmm OceanDNA-b32783/protein.faa > /dev/null
[2023-03-16 08:16:17,260] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:16:17,260] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2989b629-3809-4163-bdf0-08a85a1f30cc/OceanDNA-b32783.fa]
[2023-03-16 08:16:17,282] [INFO] Query marker FASTA was written to OceanDNA-b32783/markers.fasta
[2023-03-16 08:16:17,283] [INFO] Task started: Blastn
[2023-03-16 08:16:17,283] [INFO] Running command: blastn -query OceanDNA-b32783/markers.fasta -db /var/lib/cwl/stgcc3dbac6-8778-49e3-b28d-8c32978740d2/dqc_reference/reference_markers.fasta -out OceanDNA-b32783/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:16:17,909] [INFO] Task succeeded: Blastn
[2023-03-16 08:16:17,910] [INFO] Selected 32 target genomes.
[2023-03-16 08:16:17,910] [INFO] Target genome list was writen to OceanDNA-b32783/target_genomes.txt
[2023-03-16 08:16:18,049] [INFO] Task started: fastANI
[2023-03-16 08:16:18,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg2989b629-3809-4163-bdf0-08a85a1f30cc/OceanDNA-b32783.fa --refList OceanDNA-b32783/target_genomes.txt --output OceanDNA-b32783/fastani_result.tsv --threads 1
[2023-03-16 08:16:44,142] [INFO] Task succeeded: fastANI
[2023-03-16 08:16:44,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc3dbac6-8778-49e3-b28d-8c32978740d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:16:44,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc3dbac6-8778-49e3-b28d-8c32978740d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:16:44,158] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:16:44,158] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:16:44,159] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.5569	105	959	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.344	172	959	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.3296	126	959	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.2863	105	959	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	76.283	77	959	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.2694	129	959	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	76.2455	79	959	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.2339	106	959	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.2056	166	959	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.2028	168	959	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.178	117	959	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	76.1676	77	959	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.1623	68	959	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	76.161	77	959	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.133	123	959	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.1201	100	959	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.0647	77	959	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	76.0398	132	959	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.0276	135	959	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	75.9575	88	959	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	75.8083	64	959	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	75.7527	83	959	95	below_threshold
Fulvimarina endophytica	strain=85	GCA_003403015.1	2293836	2293836	type	True	75.7027	62	959	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	75.6833	95	959	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	75.678	50	959	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	75.6665	70	959	95	below_threshold
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	75.662	53	959	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	75.6149	70	959	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	75.3824	65	959	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:16:44,159] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32783/tc_result.tsv
[2023-03-16 08:16:44,159] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:16:44,159] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:16:44,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc3dbac6-8778-49e3-b28d-8c32978740d2/dqc_reference/checkm_data
[2023-03-16 08:16:44,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:16:44,165] [INFO] Task started: CheckM
[2023-03-16 08:16:44,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32783/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32783/checkm_input OceanDNA-b32783/checkm_result
[2023-03-16 08:17:31,136] [INFO] Task succeeded: CheckM
[2023-03-16 08:17:31,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:17:31,139] [INFO] ===== Completeness check finished =====
[2023-03-16 08:17:31,139] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:17:31,140] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32783/markers.fasta)
[2023-03-16 08:17:31,141] [INFO] Task started: Blastn
[2023-03-16 08:17:31,141] [INFO] Running command: blastn -query OceanDNA-b32783/markers.fasta -db /var/lib/cwl/stgcc3dbac6-8778-49e3-b28d-8c32978740d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32783/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:17:32,126] [INFO] Task succeeded: Blastn
[2023-03-16 08:17:32,127] [INFO] Selected 12 target genomes.
[2023-03-16 08:17:32,127] [INFO] Target genome list was writen to OceanDNA-b32783/target_genomes_gtdb.txt
[2023-03-16 08:17:32,151] [INFO] Task started: fastANI
[2023-03-16 08:17:32,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg2989b629-3809-4163-bdf0-08a85a1f30cc/OceanDNA-b32783.fa --refList OceanDNA-b32783/target_genomes_gtdb.txt --output OceanDNA-b32783/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:17:39,923] [INFO] Task succeeded: fastANI
[2023-03-16 08:17:39,930] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:17:39,930] [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_018702955.1	s__UBA8079 sp018702955	85.3423	721	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_018667335.1	s__UBA8079 sp018667335	84.1022	740	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_002727315.1	s__UBA8079 sp002727315	80.0108	368	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724635.1	s__UBA8079 sp002724635	79.6167	427	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	78.8349	346	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722515.1	s__UBA8079 sp002722515	78.2191	219	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666195.1	s__JABJAG01 sp018666195	77.5085	226	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253745.1	s__Mesorhizobium kowhaii	76.1133	94	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201075.1	s__Lichenicola cladoniae	75.8607	61	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003403015.1	s__Fulvimarina endophytica	75.7027	62	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Fulvimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498785.1	s__Sphingomonas sp902498785	75.5637	54	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:17:39,930] [INFO] GTDB search result was written to OceanDNA-b32783/result_gtdb.tsv
[2023-03-16 08:17:39,930] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:17:39,933] [INFO] DFAST_QC result json was written to OceanDNA-b32783/dqc_result.json
[2023-03-16 08:17:39,933] [INFO] DFAST_QC completed!
[2023-03-16 08:17:39,933] [INFO] Total running time: 0h1m42s