[2023-03-18 20:59:43,924] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,924] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b62892f-1c39-43ae-a322-a6af11b7ac7f/dqc_reference
[2023-03-18 20:59:45,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,685] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,685] [INFO] Running command: cat /var/lib/cwl/stgbea54d31-12aa-415c-b6d0-60ae0ff2601c/OceanDNA-b26913.fa | prodigal -d OceanDNA-b26913/cds.fna -a OceanDNA-b26913/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:59,126] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:59,127] [INFO] Task started: HMMsearch
[2023-03-18 20:59:59,127] [INFO] Running command: hmmsearch --tblout OceanDNA-b26913/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b62892f-1c39-43ae-a322-a6af11b7ac7f/dqc_reference/reference_markers.hmm OceanDNA-b26913/protein.faa > /dev/null
[2023-03-18 20:59:59,327] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:59,327] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbea54d31-12aa-415c-b6d0-60ae0ff2601c/OceanDNA-b26913.fa]
[2023-03-18 20:59:59,350] [INFO] Query marker FASTA was written to OceanDNA-b26913/markers.fasta
[2023-03-18 20:59:59,350] [INFO] Task started: Blastn
[2023-03-18 20:59:59,350] [INFO] Running command: blastn -query OceanDNA-b26913/markers.fasta -db /var/lib/cwl/stg9b62892f-1c39-43ae-a322-a6af11b7ac7f/dqc_reference/reference_markers.fasta -out OceanDNA-b26913/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:59,926] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:59,927] [INFO] Selected 20 target genomes.
[2023-03-18 20:59:59,927] [INFO] Target genome list was writen to OceanDNA-b26913/target_genomes.txt
[2023-03-18 20:59:59,936] [INFO] Task started: fastANI
[2023-03-18 20:59:59,936] [INFO] Running command: fastANI --query /var/lib/cwl/stgbea54d31-12aa-415c-b6d0-60ae0ff2601c/OceanDNA-b26913.fa --refList OceanDNA-b26913/target_genomes.txt --output OceanDNA-b26913/fastani_result.tsv --threads 1
[2023-03-18 21:00:16,815] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:16,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b62892f-1c39-43ae-a322-a6af11b7ac7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:16,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b62892f-1c39-43ae-a322-a6af11b7ac7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:16,822] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:16,822] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:00:16,822] [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
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	76.4096	58	610	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	76.2537	52	610	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	76.2007	53	610	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	76.155	51	610	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	76.0501	53	610	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	75.919	57	610	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	75.8599	56	610	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:00:16,822] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26913/tc_result.tsv
[2023-03-18 21:00:16,822] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:16,822] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:16,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b62892f-1c39-43ae-a322-a6af11b7ac7f/dqc_reference/checkm_data
[2023-03-18 21:00:16,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:16,844] [INFO] Task started: CheckM
[2023-03-18 21:00:16,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26913/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26913/checkm_input OceanDNA-b26913/checkm_result
[2023-03-18 21:00:54,785] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:54,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:54,818] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:54,819] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:54,819] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26913/markers.fasta)
[2023-03-18 21:00:54,820] [INFO] Task started: Blastn
[2023-03-18 21:00:54,820] [INFO] Running command: blastn -query OceanDNA-b26913/markers.fasta -db /var/lib/cwl/stg9b62892f-1c39-43ae-a322-a6af11b7ac7f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26913/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:55,519] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:55,523] [INFO] Selected 14 target genomes.
[2023-03-18 21:00:55,523] [INFO] Target genome list was writen to OceanDNA-b26913/target_genomes_gtdb.txt
[2023-03-18 21:00:55,536] [INFO] Task started: fastANI
[2023-03-18 21:00:55,536] [INFO] Running command: fastANI --query /var/lib/cwl/stgbea54d31-12aa-415c-b6d0-60ae0ff2601c/OceanDNA-b26913.fa --refList OceanDNA-b26913/target_genomes_gtdb.txt --output OceanDNA-b26913/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:06,848] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:06,854] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:01:06,854] [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_013214695.1	s__R2A130 sp013214695	99.0273	573	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011087605.1	s__R2A130 sp011087605	78.1305	187	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	99.98	99.97	0.98	0.98	3	-
GCA_014238155.1	s__R2A130 sp014238155	77.7566	189	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480295.1	s__R2A130 sp905480295	77.377	138	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179775.1	s__R2A130 sp000179775	76.914	85	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004017275.1	s__Mesorhizobium sp004017275	76.1099	57	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.13	97.50	0.90	0.85	4	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	75.8285	59	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_004136315.1	s__Mesorhizobium sp004136315	75.4462	57	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.54	97.14	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:06,854] [INFO] GTDB search result was written to OceanDNA-b26913/result_gtdb.tsv
[2023-03-18 21:01:06,854] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:06,855] [INFO] DFAST_QC result json was written to OceanDNA-b26913/dqc_result.json
[2023-03-18 21:01:06,855] [INFO] DFAST_QC completed!
[2023-03-18 21:01:06,855] [INFO] Total running time: 0h1m23s