[2023-03-16 00:13:32,305] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:13:32,305] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:13:32,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg617e5b2d-652a-4a55-907a-d26ad0cf6d7e/dqc_reference
[2023-03-16 00:13:33,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:13:33,523] [INFO] Task started: Prodigal
[2023-03-16 00:13:33,523] [INFO] Running command: cat /var/lib/cwl/stgf9b0af21-cee0-487d-85c6-0ba9c42133d0/OceanDNA-b34076.fa | prodigal -d OceanDNA-b34076/cds.fna -a OceanDNA-b34076/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:13:43,368] [INFO] Task succeeded: Prodigal
[2023-03-16 00:13:43,369] [INFO] Task started: HMMsearch
[2023-03-16 00:13:43,369] [INFO] Running command: hmmsearch --tblout OceanDNA-b34076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg617e5b2d-652a-4a55-907a-d26ad0cf6d7e/dqc_reference/reference_markers.hmm OceanDNA-b34076/protein.faa > /dev/null
[2023-03-16 00:13:43,570] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:13:43,570] [INFO] Found 6/6 markers.
[2023-03-16 00:13:43,587] [INFO] Query marker FASTA was written to OceanDNA-b34076/markers.fasta
[2023-03-16 00:13:43,588] [INFO] Task started: Blastn
[2023-03-16 00:13:43,588] [INFO] Running command: blastn -query OceanDNA-b34076/markers.fasta -db /var/lib/cwl/stg617e5b2d-652a-4a55-907a-d26ad0cf6d7e/dqc_reference/reference_markers.fasta -out OceanDNA-b34076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:13:44,175] [INFO] Task succeeded: Blastn
[2023-03-16 00:13:44,180] [INFO] Selected 26 target genomes.
[2023-03-16 00:13:44,181] [INFO] Target genome list was writen to OceanDNA-b34076/target_genomes.txt
[2023-03-16 00:13:44,198] [INFO] Task started: fastANI
[2023-03-16 00:13:44,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b0af21-cee0-487d-85c6-0ba9c42133d0/OceanDNA-b34076.fa --refList OceanDNA-b34076/target_genomes.txt --output OceanDNA-b34076/fastani_result.tsv --threads 1
[2023-03-16 00:13:57,572] [INFO] Task succeeded: fastANI
[2023-03-16 00:13:57,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg617e5b2d-652a-4a55-907a-d26ad0cf6d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:13:57,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg617e5b2d-652a-4a55-907a-d26ad0cf6d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:13:57,577] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:13:57,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:13:57,577] [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
Methylotenera oryzisoli	strain=La3113	GCA_004661485.1	2080758	2080758	type	True	77.2664	83	577	95	below_threshold
Methylotenera versatilis	strain=301	GCA_000093025.1	1055487	1055487	type	True	77.2064	81	577	95	below_threshold
Methylotenera mobilis	strain=JLW8	GCA_000023705.1	359408	359408	type	True	77.0738	76	577	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:13:57,580] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34076/tc_result.tsv
[2023-03-16 00:13:57,581] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:13:57,581] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:13:57,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg617e5b2d-652a-4a55-907a-d26ad0cf6d7e/dqc_reference/checkm_data
[2023-03-16 00:13:57,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:13:57,588] [INFO] Task started: CheckM
[2023-03-16 00:13:57,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34076/checkm_input OceanDNA-b34076/checkm_result
[2023-03-16 00:14:26,831] [INFO] Task succeeded: CheckM
[2023-03-16 00:14:26,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:14:26,838] [INFO] ===== Completeness check finished =====
[2023-03-16 00:14:26,838] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:14:26,838] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34076/markers.fasta)
[2023-03-16 00:14:26,839] [INFO] Task started: Blastn
[2023-03-16 00:14:26,839] [INFO] Running command: blastn -query OceanDNA-b34076/markers.fasta -db /var/lib/cwl/stg617e5b2d-652a-4a55-907a-d26ad0cf6d7e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:14:27,813] [INFO] Task succeeded: Blastn
[2023-03-16 00:14:27,816] [INFO] Selected 21 target genomes.
[2023-03-16 00:14:27,816] [INFO] Target genome list was writen to OceanDNA-b34076/target_genomes_gtdb.txt
[2023-03-16 00:14:27,839] [INFO] Task started: fastANI
[2023-03-16 00:14:27,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b0af21-cee0-487d-85c6-0ba9c42133d0/OceanDNA-b34076.fa --refList OceanDNA-b34076/target_genomes_gtdb.txt --output OceanDNA-b34076/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:14:35,583] [INFO] Task succeeded: fastANI
[2023-03-16 00:14:35,593] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:14:35,594] [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_006844635.1	s__GCA-2401735 sp006844635	78.4891	142	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__GCA-2401735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018398995.1	s__GCA-2401735 sp018398995	78.4866	205	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__GCA-2401735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401735.1	s__GCA-2401735 sp002401735	78.1923	156	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__GCA-2401735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857755.1	s__GCA-2401735 sp017857755	78.1342	210	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__GCA-2401735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384375.1	s__Methylotenera_A versatilis_B	77.251	94	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002429455.1	s__Methylotenera sp002429455	77.1813	50	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903846555.1	s__Methylotenera sp903846555	77.1523	79	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744605.1	s__Methylotenera sp000744605	77.0494	82	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799165.1	s__Methylotenera_A versatilis_A	77.0368	88	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281475.1	s__Methylophilus sp002281475	77.0347	68	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	99.39	99.39	0.85	0.85	2	-
GCA_002083635.1	s__Methylotenera_A sp002083635	76.9182	106	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera_A	95.0	96.09	95.78	0.91	0.88	3	-
GCA_001803395.1	s__Methylotenera sp001803395	76.8752	73	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140755.1	s__Methylotenera sp013140755	76.841	81	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838125.1	s__Methylotenera sp903838125	76.8406	70	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.83	99.83	0.90	0.90	2	-
GCA_013141075.1	s__Methylotenera sp013141075	76.8067	87	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	97.66	97.66	0.85	0.85	2	-
GCA_013141425.1	s__Methylotenera sp013141425	76.759	67	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378845.1	s__Methylotenera_A sp014378845	76.4035	72	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903854305.1	s__Methylotenera sp903854305	76.0575	59	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:14:35,596] [INFO] GTDB search result was written to OceanDNA-b34076/result_gtdb.tsv
[2023-03-16 00:14:35,599] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:14:35,602] [INFO] DFAST_QC result json was written to OceanDNA-b34076/dqc_result.json
[2023-03-16 00:14:35,602] [INFO] DFAST_QC completed!
[2023-03-16 00:14:35,602] [INFO] Total running time: 0h1m3s