[2023-03-14 12:48:35,577] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:48:35,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:48:35,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd81a52a-6180-4a54-ad66-f3b7bacbf04a/dqc_reference
[2023-03-14 12:48:37,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:48:37,138] [INFO] Task started: Prodigal
[2023-03-14 12:48:37,138] [INFO] Running command: cat /var/lib/cwl/stg343ca870-64f3-4007-9c89-e82d866b3f76/OceanDNA-b27695.fa | prodigal -d OceanDNA-b27695/cds.fna -a OceanDNA-b27695/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:48:47,111] [INFO] Task succeeded: Prodigal
[2023-03-14 12:48:47,111] [INFO] Task started: HMMsearch
[2023-03-14 12:48:47,111] [INFO] Running command: hmmsearch --tblout OceanDNA-b27695/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd81a52a-6180-4a54-ad66-f3b7bacbf04a/dqc_reference/reference_markers.hmm OceanDNA-b27695/protein.faa > /dev/null
[2023-03-14 12:48:47,338] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:48:47,339] [INFO] Found 6/6 markers.
[2023-03-14 12:48:47,356] [INFO] Query marker FASTA was written to OceanDNA-b27695/markers.fasta
[2023-03-14 12:48:47,357] [INFO] Task started: Blastn
[2023-03-14 12:48:47,357] [INFO] Running command: blastn -query OceanDNA-b27695/markers.fasta -db /var/lib/cwl/stgbd81a52a-6180-4a54-ad66-f3b7bacbf04a/dqc_reference/reference_markers.fasta -out OceanDNA-b27695/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:48:48,309] [INFO] Task succeeded: Blastn
[2023-03-14 12:48:48,310] [INFO] Selected 25 target genomes.
[2023-03-14 12:48:48,310] [INFO] Target genome list was writen to OceanDNA-b27695/target_genomes.txt
[2023-03-14 12:48:48,328] [INFO] Task started: fastANI
[2023-03-14 12:48:48,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg343ca870-64f3-4007-9c89-e82d866b3f76/OceanDNA-b27695.fa --refList OceanDNA-b27695/target_genomes.txt --output OceanDNA-b27695/fastani_result.tsv --threads 1
[2023-03-14 12:49:00,002] [INFO] Task succeeded: fastANI
[2023-03-14 12:49:00,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd81a52a-6180-4a54-ad66-f3b7bacbf04a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:49:00,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd81a52a-6180-4a54-ad66-f3b7bacbf04a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:49:00,003] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:49:00,003] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:49:00,003] [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
--------------------------------------------------------------------------------
[2023-03-14 12:49:00,004] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27695/tc_result.tsv
[2023-03-14 12:49:00,004] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:49:00,004] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:49:00,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd81a52a-6180-4a54-ad66-f3b7bacbf04a/dqc_reference/checkm_data
[2023-03-14 12:49:00,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:49:00,043] [INFO] Task started: CheckM
[2023-03-14 12:49:00,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27695/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27695/checkm_input OceanDNA-b27695/checkm_result
[2023-03-14 12:49:33,202] [INFO] Task succeeded: CheckM
[2023-03-14 12:49:33,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.55%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:49:33,205] [INFO] ===== Completeness check finished =====
[2023-03-14 12:49:33,205] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:49:33,206] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27695/markers.fasta)
[2023-03-14 12:49:33,207] [INFO] Task started: Blastn
[2023-03-14 12:49:33,207] [INFO] Running command: blastn -query OceanDNA-b27695/markers.fasta -db /var/lib/cwl/stgbd81a52a-6180-4a54-ad66-f3b7bacbf04a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27695/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:49:34,147] [INFO] Task succeeded: Blastn
[2023-03-14 12:49:34,149] [INFO] Selected 18 target genomes.
[2023-03-14 12:49:34,149] [INFO] Target genome list was writen to OceanDNA-b27695/target_genomes_gtdb.txt
[2023-03-14 12:49:34,171] [INFO] Task started: fastANI
[2023-03-14 12:49:34,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg343ca870-64f3-4007-9c89-e82d866b3f76/OceanDNA-b27695.fa --refList OceanDNA-b27695/target_genomes_gtdb.txt --output OceanDNA-b27695/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:49:41,453] [INFO] Task succeeded: fastANI
[2023-03-14 12:49:41,457] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:49:41,457] [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_905182285.1	s__Amylibacter sp905182285	99.441	550	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.59	99.59	0.86	0.86	2	conclusive
GCA_000153745.1	s__Amylibacter sp000153745	81.3278	473	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	98.38	97.19	0.95	0.89	11	-
GCA_900197625.1	s__Amylibacter sp900197625	80.7409	424	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.40	99.20	0.94	0.94	3	-
GCA_905181935.1	s__Amylibacter sp905181935	77.9727	235	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:49:41,458] [INFO] GTDB search result was written to OceanDNA-b27695/result_gtdb.tsv
[2023-03-14 12:49:41,458] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:49:41,459] [INFO] DFAST_QC result json was written to OceanDNA-b27695/dqc_result.json
[2023-03-14 12:49:41,460] [INFO] DFAST_QC completed!
[2023-03-14 12:49:41,460] [INFO] Total running time: 0h1m6s