[2023-03-19 03:36:54,164] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:36:54,165] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:36:54,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg952e3cbd-d695-45d7-8e4c-acf6d14e05af/dqc_reference
[2023-03-19 03:36:55,316] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:36:55,316] [INFO] Task started: Prodigal
[2023-03-19 03:36:55,316] [INFO] Running command: cat /var/lib/cwl/stg3c186511-611a-42d3-87ac-4f9845488125/OceanDNA-b33287.fa | prodigal -d OceanDNA-b33287/cds.fna -a OceanDNA-b33287/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:37:07,133] [INFO] Task succeeded: Prodigal
[2023-03-19 03:37:07,133] [INFO] Task started: HMMsearch
[2023-03-19 03:37:07,133] [INFO] Running command: hmmsearch --tblout OceanDNA-b33287/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg952e3cbd-d695-45d7-8e4c-acf6d14e05af/dqc_reference/reference_markers.hmm OceanDNA-b33287/protein.faa > /dev/null
[2023-03-19 03:37:07,300] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:37:07,301] [INFO] Found 6/6 markers.
[2023-03-19 03:37:07,317] [INFO] Query marker FASTA was written to OceanDNA-b33287/markers.fasta
[2023-03-19 03:37:07,318] [INFO] Task started: Blastn
[2023-03-19 03:37:07,318] [INFO] Running command: blastn -query OceanDNA-b33287/markers.fasta -db /var/lib/cwl/stg952e3cbd-d695-45d7-8e4c-acf6d14e05af/dqc_reference/reference_markers.fasta -out OceanDNA-b33287/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:37:07,875] [INFO] Task succeeded: Blastn
[2023-03-19 03:37:07,876] [INFO] Selected 6 target genomes.
[2023-03-19 03:37:07,876] [INFO] Target genome list was writen to OceanDNA-b33287/target_genomes.txt
[2023-03-19 03:37:07,881] [INFO] Task started: fastANI
[2023-03-19 03:37:07,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c186511-611a-42d3-87ac-4f9845488125/OceanDNA-b33287.fa --refList OceanDNA-b33287/target_genomes.txt --output OceanDNA-b33287/fastani_result.tsv --threads 1
[2023-03-19 03:37:11,781] [INFO] Task succeeded: fastANI
[2023-03-19 03:37:11,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg952e3cbd-d695-45d7-8e4c-acf6d14e05af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:37:11,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg952e3cbd-d695-45d7-8e4c-acf6d14e05af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:37:11,787] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:37:11,787] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:37:11,788] [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
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	90.1859	529	574	95	below_threshold
Alcaligenes faecalis	strain=DSM 30030	GCA_002443155.1	511	511	type	True	90.1774	530	574	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_000739855.1	32001	511	type	True	90.1636	533	574	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_001748345.1	32001	511	type	True	90.109	537	574	95	below_threshold
Alcaligenes ammonioxydans	strain=HO-1	GCA_019343455.1	2582914	2582914	type	True	85.7932	486	574	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	85.677	506	574	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:37:11,788] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33287/tc_result.tsv
[2023-03-19 03:37:11,788] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:37:11,788] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:37:11,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg952e3cbd-d695-45d7-8e4c-acf6d14e05af/dqc_reference/checkm_data
[2023-03-19 03:37:11,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:37:11,901] [INFO] Task started: CheckM
[2023-03-19 03:37:11,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33287/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33287/checkm_input OceanDNA-b33287/checkm_result
[2023-03-19 03:37:45,781] [INFO] Task succeeded: CheckM
[2023-03-19 03:37:45,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.65%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:37:45,784] [INFO] ===== Completeness check finished =====
[2023-03-19 03:37:45,784] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:37:45,784] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33287/markers.fasta)
[2023-03-19 03:37:45,785] [INFO] Task started: Blastn
[2023-03-19 03:37:45,785] [INFO] Running command: blastn -query OceanDNA-b33287/markers.fasta -db /var/lib/cwl/stg952e3cbd-d695-45d7-8e4c-acf6d14e05af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33287/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:37:46,615] [INFO] Task succeeded: Blastn
[2023-03-19 03:37:46,616] [INFO] Selected 7 target genomes.
[2023-03-19 03:37:46,616] [INFO] Target genome list was writen to OceanDNA-b33287/target_genomes_gtdb.txt
[2023-03-19 03:37:46,622] [INFO] Task started: fastANI
[2023-03-19 03:37:46,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c186511-611a-42d3-87ac-4f9845488125/OceanDNA-b33287.fa --refList OceanDNA-b33287/target_genomes_gtdb.txt --output OceanDNA-b33287/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:37:51,642] [INFO] Task succeeded: fastANI
[2023-03-19 03:37:51,647] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:37:51,647] [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
GCF_003076515.1	s__Alcaligenes aquatilis	96.3862	542	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.23	96.52	0.93	0.89	8	conclusive
GCF_002443155.1	s__Alcaligenes faecalis	90.1774	530	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.39	97.71	0.93	0.90	22	-
GCF_009497775.1	s__Alcaligenes faecalis_D	89.9354	528	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005311025.1	s__Alcaligenes phenolicus	89.241	531	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	97.79	96.15	0.91	0.86	11	-
GCF_017377875.1	s__Alcaligenes sp017377875	87.8199	527	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004319585.1	s__Alcaligenes faecalis_C	85.7463	494	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	99.29	99.23	0.95	0.93	4	-
GCF_014652815.1	s__Alcaligenes pakistanensis	85.677	506	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	99.29	99.08	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-19 03:37:51,647] [INFO] GTDB search result was written to OceanDNA-b33287/result_gtdb.tsv
[2023-03-19 03:37:51,647] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:37:51,648] [INFO] DFAST_QC result json was written to OceanDNA-b33287/dqc_result.json
[2023-03-19 03:37:51,648] [INFO] DFAST_QC completed!
[2023-03-19 03:37:51,648] [INFO] Total running time: 0h0m57s