[2023-03-18 04:54:25,331] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:54:25,332] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:54:25,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg8737bc82-1566-403a-8240-d35e6e2566f5/dqc_reference
[2023-03-18 04:54:26,988] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:54:26,989] [INFO] Task started: Prodigal
[2023-03-18 04:54:26,989] [INFO] Running command: cat /var/lib/cwl/stg2695e74e-4d1a-42ed-aafd-73a6aef0e54b/OceanDNA-b34088.fa | prodigal -d OceanDNA-b34088/cds.fna -a OceanDNA-b34088/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:54:38,441] [INFO] Task succeeded: Prodigal
[2023-03-18 04:54:38,441] [INFO] Task started: HMMsearch
[2023-03-18 04:54:38,442] [INFO] Running command: hmmsearch --tblout OceanDNA-b34088/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8737bc82-1566-403a-8240-d35e6e2566f5/dqc_reference/reference_markers.hmm OceanDNA-b34088/protein.faa > /dev/null
[2023-03-18 04:54:38,609] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:54:38,610] [INFO] Found 6/6 markers.
[2023-03-18 04:54:38,624] [INFO] Query marker FASTA was written to OceanDNA-b34088/markers.fasta
[2023-03-18 04:54:38,624] [INFO] Task started: Blastn
[2023-03-18 04:54:38,624] [INFO] Running command: blastn -query OceanDNA-b34088/markers.fasta -db /var/lib/cwl/stg8737bc82-1566-403a-8240-d35e6e2566f5/dqc_reference/reference_markers.fasta -out OceanDNA-b34088/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:54:39,151] [INFO] Task succeeded: Blastn
[2023-03-18 04:54:39,152] [INFO] Selected 28 target genomes.
[2023-03-18 04:54:39,152] [INFO] Target genome list was writen to OceanDNA-b34088/target_genomes.txt
[2023-03-18 04:54:39,171] [INFO] Task started: fastANI
[2023-03-18 04:54:39,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg2695e74e-4d1a-42ed-aafd-73a6aef0e54b/OceanDNA-b34088.fa --refList OceanDNA-b34088/target_genomes.txt --output OceanDNA-b34088/fastani_result.tsv --threads 1
[2023-03-18 04:54:51,200] [INFO] Task succeeded: fastANI
[2023-03-18 04:54:51,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8737bc82-1566-403a-8240-d35e6e2566f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:54:51,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8737bc82-1566-403a-8240-d35e6e2566f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:54:51,206] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:54:51,206] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:54:51,206] [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 versatilis	strain=301	GCA_000093025.1	1055487	1055487	type	True	77.0631	111	685	95	below_threshold
Methylotenera mobilis	strain=JLW8	GCA_000023705.1	359408	359408	type	True	76.7189	98	685	95	below_threshold
Methylophilus methylotrophus	strain=ATCC 53528	GCA_000378225.1	17	17	type	True	76.3093	57	685	95	below_threshold
Methyloradius palustris	strain=Zm11	GCA_019703875.1	2778876	2778876	type	True	76.1941	50	685	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:54:51,207] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34088/tc_result.tsv
[2023-03-18 04:54:51,207] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:54:51,207] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:54:51,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8737bc82-1566-403a-8240-d35e6e2566f5/dqc_reference/checkm_data
[2023-03-18 04:54:51,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:54:51,463] [INFO] Task started: CheckM
[2023-03-18 04:54:51,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34088/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34088/checkm_input OceanDNA-b34088/checkm_result
[2023-03-18 04:55:23,992] [INFO] Task succeeded: CheckM
[2023-03-18 04:55:23,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:55:24,055] [INFO] ===== Completeness check finished =====
[2023-03-18 04:55:24,055] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:55:24,055] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34088/markers.fasta)
[2023-03-18 04:55:24,056] [INFO] Task started: Blastn
[2023-03-18 04:55:24,057] [INFO] Running command: blastn -query OceanDNA-b34088/markers.fasta -db /var/lib/cwl/stg8737bc82-1566-403a-8240-d35e6e2566f5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34088/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:55:24,827] [INFO] Task succeeded: Blastn
[2023-03-18 04:55:24,846] [INFO] Selected 17 target genomes.
[2023-03-18 04:55:24,846] [INFO] Target genome list was writen to OceanDNA-b34088/target_genomes_gtdb.txt
[2023-03-18 04:55:24,867] [INFO] Task started: fastANI
[2023-03-18 04:55:24,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg2695e74e-4d1a-42ed-aafd-73a6aef0e54b/OceanDNA-b34088.fa --refList OceanDNA-b34088/target_genomes_gtdb.txt --output OceanDNA-b34088/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:55:31,837] [INFO] Task succeeded: fastANI
[2023-03-18 04:55:31,847] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:55:31,847] [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_018398995.1	s__GCA-2401735 sp018398995	80.7004	387	685	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	78.8357	226	685	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	78.11	176	685	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_006844635.1	s__GCA-2401735 sp006844635	77.7998	143	685	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_002083635.1	s__Methylotenera_A sp002083635	77.1198	121	685	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_000525025.1	s__Methylophilus sp000525025	77.0886	109	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	98.40	98.39	0.92	0.91	3	-
GCA_013140755.1	s__Methylotenera sp013140755	77.0195	85	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903926935.1	s__Methylotenera sp903926935	76.9933	90	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141425.1	s__Methylotenera sp013141425	76.8156	88	685	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	76.8081	95	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876765.1	s__Methylotenera sp903876765	76.783	72	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.98	99.97	0.97	0.96	3	-
GCA_903882525.1	s__Methylotenera sp903882525	76.7106	59	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.32	98.82	0.88	0.81	23	-
GCA_002414145.1	s__Methylophilus sp002414145	76.629	97	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	99.56	99.56	0.92	0.92	2	-
GCA_013141075.1	s__Methylotenera sp013141075	76.5186	104	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	97.66	97.66	0.85	0.85	2	-
GCA_903854305.1	s__Methylotenera sp903854305	76.0576	82	685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:55:31,850] [INFO] GTDB search result was written to OceanDNA-b34088/result_gtdb.tsv
[2023-03-18 04:55:31,851] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:55:31,852] [INFO] DFAST_QC result json was written to OceanDNA-b34088/dqc_result.json
[2023-03-18 04:55:31,852] [INFO] DFAST_QC completed!
[2023-03-18 04:55:31,852] [INFO] Total running time: 0h1m7s