[2023-03-15 06:28:21,343] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,343] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,343] [INFO] DQC Reference Directory: /var/lib/cwl/stge6ce81e6-8397-43a3-8510-3f677c285a28/dqc_reference
[2023-03-15 06:28:22,456] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,457] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,457] [INFO] Running command: cat /var/lib/cwl/stg4dd1378d-4662-477d-b8d3-3597f0433538/OceanDNA-b21328.fa | prodigal -d OceanDNA-b21328/cds.fna -a OceanDNA-b21328/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:33,064] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:33,064] [INFO] Task started: HMMsearch
[2023-03-15 06:28:33,064] [INFO] Running command: hmmsearch --tblout OceanDNA-b21328/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6ce81e6-8397-43a3-8510-3f677c285a28/dqc_reference/reference_markers.hmm OceanDNA-b21328/protein.faa > /dev/null
[2023-03-15 06:28:33,253] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:33,253] [INFO] Found 6/6 markers.
[2023-03-15 06:28:33,268] [INFO] Query marker FASTA was written to OceanDNA-b21328/markers.fasta
[2023-03-15 06:28:33,268] [INFO] Task started: Blastn
[2023-03-15 06:28:33,268] [INFO] Running command: blastn -query OceanDNA-b21328/markers.fasta -db /var/lib/cwl/stge6ce81e6-8397-43a3-8510-3f677c285a28/dqc_reference/reference_markers.fasta -out OceanDNA-b21328/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:33,830] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:33,836] [INFO] Selected 23 target genomes.
[2023-03-15 06:28:33,837] [INFO] Target genome list was writen to OceanDNA-b21328/target_genomes.txt
[2023-03-15 06:28:33,850] [INFO] Task started: fastANI
[2023-03-15 06:28:33,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dd1378d-4662-477d-b8d3-3597f0433538/OceanDNA-b21328.fa --refList OceanDNA-b21328/target_genomes.txt --output OceanDNA-b21328/fastani_result.tsv --threads 1
[2023-03-15 06:28:45,302] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:45,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6ce81e6-8397-43a3-8510-3f677c285a28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:45,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6ce81e6-8397-43a3-8510-3f677c285a28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:45,303] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:45,303] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:28:45,303] [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
--------------------------------------------------------------------------------
[2023-03-15 06:28:45,303] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21328/tc_result.tsv
[2023-03-15 06:28:45,303] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:45,303] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:45,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6ce81e6-8397-43a3-8510-3f677c285a28/dqc_reference/checkm_data
[2023-03-15 06:28:45,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:45,310] [INFO] Task started: CheckM
[2023-03-15 06:28:45,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21328/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21328/checkm_input OceanDNA-b21328/checkm_result
[2023-03-15 06:29:16,297] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:16,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:16,348] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:16,349] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:16,349] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21328/markers.fasta)
[2023-03-15 06:29:16,349] [INFO] Task started: Blastn
[2023-03-15 06:29:16,349] [INFO] Running command: blastn -query OceanDNA-b21328/markers.fasta -db /var/lib/cwl/stge6ce81e6-8397-43a3-8510-3f677c285a28/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21328/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:17,304] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:17,309] [INFO] Selected 19 target genomes.
[2023-03-15 06:29:17,309] [INFO] Target genome list was writen to OceanDNA-b21328/target_genomes_gtdb.txt
[2023-03-15 06:29:17,320] [INFO] Task started: fastANI
[2023-03-15 06:29:17,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dd1378d-4662-477d-b8d3-3597f0433538/OceanDNA-b21328.fa --refList OceanDNA-b21328/target_genomes_gtdb.txt --output OceanDNA-b21328/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:24,859] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:24,866] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 06:29:24,866] [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_009873655.1	s__UBA8687 sp009873655	99.4638	565	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	99.50	99.47	0.94	0.93	3	conclusive
GCA_018665625.1	s__UBA8687 sp018665625	77.7563	243	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349585.1	s__UBA8687 sp013349585	77.7524	215	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009873635.1	s__LS-NOB sp009873635	77.255	82	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.03	98.80	0.95	0.93	3	-
GCA_002697825.1	s__UBA8687 sp002697825	77.1046	122	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001542995.1	s__LS-NOB sp001542995	76.3009	92	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786505.1	s__LS-NOB sp002786505	76.0692	66	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382285.1	s__LS-NOB sp014382285	76.0512	79	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_018653085.1	s__LS-NOB sp018653085	75.8563	94	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_018664975.1	s__LS-NOB sp018664975	75.7186	54	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018702695.1	s__LS-NOB sp018702695	75.6935	52	603	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.34	99.32	0.82	0.80	4	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:24,866] [INFO] GTDB search result was written to OceanDNA-b21328/result_gtdb.tsv
[2023-03-15 06:29:24,866] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:24,867] [INFO] DFAST_QC result json was written to OceanDNA-b21328/dqc_result.json
[2023-03-15 06:29:24,867] [INFO] DFAST_QC completed!
[2023-03-15 06:29:24,867] [INFO] Total running time: 0h1m4s