[2023-03-15 23:15:05,776] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:15:05,777] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:15:05,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a4f061b-a4c8-41e5-b348-355971ecba62/dqc_reference
[2023-03-15 23:15:07,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:15:07,541] [INFO] Task started: Prodigal
[2023-03-15 23:15:07,541] [INFO] Running command: cat /var/lib/cwl/stg3c72e9b4-6a09-4767-8bdc-bad1a4c0ad22/OceanDNA-b32786.fa | prodigal -d OceanDNA-b32786/cds.fna -a OceanDNA-b32786/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:15:21,555] [INFO] Task succeeded: Prodigal
[2023-03-15 23:15:21,555] [INFO] Task started: HMMsearch
[2023-03-15 23:15:21,555] [INFO] Running command: hmmsearch --tblout OceanDNA-b32786/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a4f061b-a4c8-41e5-b348-355971ecba62/dqc_reference/reference_markers.hmm OceanDNA-b32786/protein.faa > /dev/null
[2023-03-15 23:15:21,716] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:15:21,717] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c72e9b4-6a09-4767-8bdc-bad1a4c0ad22/OceanDNA-b32786.fa]
[2023-03-15 23:15:21,734] [INFO] Query marker FASTA was written to OceanDNA-b32786/markers.fasta
[2023-03-15 23:15:21,735] [INFO] Task started: Blastn
[2023-03-15 23:15:21,735] [INFO] Running command: blastn -query OceanDNA-b32786/markers.fasta -db /var/lib/cwl/stg6a4f061b-a4c8-41e5-b348-355971ecba62/dqc_reference/reference_markers.fasta -out OceanDNA-b32786/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:22,344] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:22,345] [INFO] Selected 30 target genomes.
[2023-03-15 23:15:22,346] [INFO] Target genome list was writen to OceanDNA-b32786/target_genomes.txt
[2023-03-15 23:15:22,390] [INFO] Task started: fastANI
[2023-03-15 23:15:22,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c72e9b4-6a09-4767-8bdc-bad1a4c0ad22/OceanDNA-b32786.fa --refList OceanDNA-b32786/target_genomes.txt --output OceanDNA-b32786/fastani_result.tsv --threads 1
[2023-03-15 23:15:44,956] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:44,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a4f061b-a4c8-41e5-b348-355971ecba62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:15:44,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a4f061b-a4c8-41e5-b348-355971ecba62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:15:44,969] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:15:44,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:15:44,970] [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
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.2676	88	761	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.2579	105	761	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.2244	107	761	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.1533	71	761	95	below_threshold
Zavarzinia aquatilis	strain=HR-AS	GCA_003173035.1	2211142	2211142	type	True	76.1398	65	761	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.9914	97	761	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.9475	75	761	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.9299	91	761	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	75.9074	69	761	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.8635	89	761	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	75.7818	60	761	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.7681	100	761	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.6281	61	761	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	75.6138	81	761	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.6088	87	761	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.6002	90	761	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.574	71	761	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.4855	65	761	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.3962	68	761	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	75.2197	51	761	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	75.2036	52	761	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:15:44,970] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32786/tc_result.tsv
[2023-03-15 23:15:44,972] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:15:44,972] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:15:44,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a4f061b-a4c8-41e5-b348-355971ecba62/dqc_reference/checkm_data
[2023-03-15 23:15:44,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:15:44,977] [INFO] Task started: CheckM
[2023-03-15 23:15:44,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32786/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32786/checkm_input OceanDNA-b32786/checkm_result
[2023-03-15 23:16:22,532] [INFO] Task succeeded: CheckM
[2023-03-15 23:16:22,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 1.14%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:16:22,538] [INFO] ===== Completeness check finished =====
[2023-03-15 23:16:22,538] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:16:22,538] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32786/markers.fasta)
[2023-03-15 23:16:22,539] [INFO] Task started: Blastn
[2023-03-15 23:16:22,540] [INFO] Running command: blastn -query OceanDNA-b32786/markers.fasta -db /var/lib/cwl/stg6a4f061b-a4c8-41e5-b348-355971ecba62/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32786/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:16:23,536] [INFO] Task succeeded: Blastn
[2023-03-15 23:16:23,540] [INFO] Selected 11 target genomes.
[2023-03-15 23:16:23,540] [INFO] Target genome list was writen to OceanDNA-b32786/target_genomes_gtdb.txt
[2023-03-15 23:16:23,551] [INFO] Task started: fastANI
[2023-03-15 23:16:23,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c72e9b4-6a09-4767-8bdc-bad1a4c0ad22/OceanDNA-b32786.fa --refList OceanDNA-b32786/target_genomes_gtdb.txt --output OceanDNA-b32786/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:16:29,764] [INFO] Task succeeded: fastANI
[2023-03-15 23:16:29,769] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:16:29,770] [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_002724635.1	s__UBA8079 sp002724635	99.8852	717	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002727315.1	s__UBA8079 sp002727315	80.3631	295	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667335.1	s__UBA8079 sp018667335	79.264	479	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_018702955.1	s__UBA8079 sp018702955	79.0856	462	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_002722515.1	s__UBA8079 sp002722515	77.9203	249	761	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	77.8057	255	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666195.1	s__JABJAG01 sp018666195	76.4423	144	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:16:29,772] [INFO] GTDB search result was written to OceanDNA-b32786/result_gtdb.tsv
[2023-03-15 23:16:29,774] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:16:29,777] [INFO] DFAST_QC result json was written to OceanDNA-b32786/dqc_result.json
[2023-03-15 23:16:29,777] [INFO] DFAST_QC completed!
[2023-03-15 23:16:29,777] [INFO] Total running time: 0h1m24s