[2023-03-18 20:13:32,807] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,807] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg01961f4b-9cfa-45dd-8191-0e6e4049101b/dqc_reference
[2023-03-18 20:13:34,556] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:34,556] [INFO] Task started: Prodigal
[2023-03-18 20:13:34,557] [INFO] Running command: cat /var/lib/cwl/stg4863f75b-6549-485c-a5a0-5222e4f2e3f6/OceanDNA-b24517.fa | prodigal -d OceanDNA-b24517/cds.fna -a OceanDNA-b24517/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:39,990] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:39,990] [INFO] Task started: HMMsearch
[2023-03-18 20:13:39,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b24517/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01961f4b-9cfa-45dd-8191-0e6e4049101b/dqc_reference/reference_markers.hmm OceanDNA-b24517/protein.faa > /dev/null
[2023-03-18 20:13:40,135] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:40,135] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4863f75b-6549-485c-a5a0-5222e4f2e3f6/OceanDNA-b24517.fa]
[2023-03-18 20:13:40,145] [INFO] Query marker FASTA was written to OceanDNA-b24517/markers.fasta
[2023-03-18 20:13:40,145] [INFO] Task started: Blastn
[2023-03-18 20:13:40,145] [INFO] Running command: blastn -query OceanDNA-b24517/markers.fasta -db /var/lib/cwl/stg01961f4b-9cfa-45dd-8191-0e6e4049101b/dqc_reference/reference_markers.fasta -out OceanDNA-b24517/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:40,644] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:40,645] [INFO] Selected 13 target genomes.
[2023-03-18 20:13:40,645] [INFO] Target genome list was writen to OceanDNA-b24517/target_genomes.txt
[2023-03-18 20:13:40,651] [INFO] Task started: fastANI
[2023-03-18 20:13:40,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg4863f75b-6549-485c-a5a0-5222e4f2e3f6/OceanDNA-b24517.fa --refList OceanDNA-b24517/target_genomes.txt --output OceanDNA-b24517/fastani_result.tsv --threads 1
[2023-03-18 20:13:44,058] [INFO] Task succeeded: fastANI
[2023-03-18 20:13:44,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01961f4b-9cfa-45dd-8191-0e6e4049101b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:13:44,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01961f4b-9cfa-45dd-8191-0e6e4049101b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:13:44,059] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:13:44,059] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:13:44,059] [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
--------------------------------------------------------------------------------
[2023-03-18 20:13:44,059] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24517/tc_result.tsv
[2023-03-18 20:13:44,059] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:13:44,059] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:13:44,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01961f4b-9cfa-45dd-8191-0e6e4049101b/dqc_reference/checkm_data
[2023-03-18 20:13:44,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:13:44,155] [INFO] Task started: CheckM
[2023-03-18 20:13:44,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24517/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24517/checkm_input OceanDNA-b24517/checkm_result
[2023-03-18 20:14:05,432] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:05,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:05,434] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:05,434] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:05,434] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24517/markers.fasta)
[2023-03-18 20:14:05,435] [INFO] Task started: Blastn
[2023-03-18 20:14:05,435] [INFO] Running command: blastn -query OceanDNA-b24517/markers.fasta -db /var/lib/cwl/stg01961f4b-9cfa-45dd-8191-0e6e4049101b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24517/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:06,108] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:06,109] [INFO] Selected 15 target genomes.
[2023-03-18 20:14:06,109] [INFO] Target genome list was writen to OceanDNA-b24517/target_genomes_gtdb.txt
[2023-03-18 20:14:06,470] [INFO] Task started: fastANI
[2023-03-18 20:14:06,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg4863f75b-6549-485c-a5a0-5222e4f2e3f6/OceanDNA-b24517.fa --refList OceanDNA-b24517/target_genomes_gtdb.txt --output OceanDNA-b24517/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:14:09,805] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:09,812] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:14:09,813] [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_004321805.1	s__HIMB59 sp004321805	99.0574	232	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002169365.1	s__HIMB59 sp002169365	82.7367	113	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522585.1	s__HIMB59 sp902522585	79.6709	91	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529795.1	s__HIMB59 sp902529795	79.249	104	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000299115.1	s__HIMB59 sp000299115	78.6742	142	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638215.1	s__HIMB59 sp008638215	78.4659	115	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.46	99.38	0.89	0.85	4	-
GCA_902521465.1	s__HIMB59 sp902521465	77.9489	120	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.86	99.86	0.95	0.95	2	-
GCA_902575065.1	s__HIMB59 sp902575065	77.9057	108	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	97.83	97.83	0.83	0.83	2	-
GCA_902546975.1	s__HIMB59 sp902546975	77.6829	103	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.15	95.57	0.84	0.81	5	-
GCA_902611415.1	s__HIMB59 sp902611415	77.6095	106	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591315.1	s__HIMB59 sp902591315	77.4836	87	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.30	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:14:09,813] [INFO] GTDB search result was written to OceanDNA-b24517/result_gtdb.tsv
[2023-03-18 20:14:09,813] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:14:09,814] [INFO] DFAST_QC result json was written to OceanDNA-b24517/dqc_result.json
[2023-03-18 20:14:09,814] [INFO] DFAST_QC completed!
[2023-03-18 20:14:09,814] [INFO] Total running time: 0h0m37s