[2023-03-18 07:54:29,602] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:29,602] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:29,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg37afcf86-5437-4013-a77c-5761f90fd6b5/dqc_reference
[2023-03-18 07:54:30,714] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:30,714] [INFO] Task started: Prodigal
[2023-03-18 07:54:30,714] [INFO] Running command: cat /var/lib/cwl/stge907bd51-b907-41dd-8fd9-38d589debdc6/OceanDNA-b112.fa | prodigal -d OceanDNA-b112/cds.fna -a OceanDNA-b112/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:42,463] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:42,463] [INFO] Task started: HMMsearch
[2023-03-18 07:54:42,463] [INFO] Running command: hmmsearch --tblout OceanDNA-b112/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37afcf86-5437-4013-a77c-5761f90fd6b5/dqc_reference/reference_markers.hmm OceanDNA-b112/protein.faa > /dev/null
[2023-03-18 07:54:42,614] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:42,615] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge907bd51-b907-41dd-8fd9-38d589debdc6/OceanDNA-b112.fa]
[2023-03-18 07:54:42,630] [INFO] Query marker FASTA was written to OceanDNA-b112/markers.fasta
[2023-03-18 07:54:42,632] [INFO] Task started: Blastn
[2023-03-18 07:54:42,632] [INFO] Running command: blastn -query OceanDNA-b112/markers.fasta -db /var/lib/cwl/stg37afcf86-5437-4013-a77c-5761f90fd6b5/dqc_reference/reference_markers.fasta -out OceanDNA-b112/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:43,140] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:43,142] [INFO] Selected 9 target genomes.
[2023-03-18 07:54:43,142] [INFO] Target genome list was writen to OceanDNA-b112/target_genomes.txt
[2023-03-18 07:54:43,147] [INFO] Task started: fastANI
[2023-03-18 07:54:43,147] [INFO] Running command: fastANI --query /var/lib/cwl/stge907bd51-b907-41dd-8fd9-38d589debdc6/OceanDNA-b112.fa --refList OceanDNA-b112/target_genomes.txt --output OceanDNA-b112/fastani_result.tsv --threads 1
[2023-03-18 07:54:49,928] [INFO] Task succeeded: fastANI
[2023-03-18 07:54:49,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37afcf86-5437-4013-a77c-5761f90fd6b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:54:49,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37afcf86-5437-4013-a77c-5761f90fd6b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:54:49,929] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:54:49,929] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:54:49,929] [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 07:54:49,930] [INFO] DFAST Taxonomy check result was written to OceanDNA-b112/tc_result.tsv
[2023-03-18 07:54:49,930] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:54:49,930] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:54:49,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37afcf86-5437-4013-a77c-5761f90fd6b5/dqc_reference/checkm_data
[2023-03-18 07:54:49,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:54:49,938] [INFO] Task started: CheckM
[2023-03-18 07:54:49,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b112/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b112/checkm_input OceanDNA-b112/checkm_result
[2023-03-18 07:55:22,396] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:22,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:55:22,399] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:22,399] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:22,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b112/markers.fasta)
[2023-03-18 07:55:22,400] [INFO] Task started: Blastn
[2023-03-18 07:55:22,400] [INFO] Running command: blastn -query OceanDNA-b112/markers.fasta -db /var/lib/cwl/stg37afcf86-5437-4013-a77c-5761f90fd6b5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b112/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:23,077] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:23,078] [INFO] Selected 12 target genomes.
[2023-03-18 07:55:23,078] [INFO] Target genome list was writen to OceanDNA-b112/target_genomes_gtdb.txt
[2023-03-18 07:55:23,147] [INFO] Task started: fastANI
[2023-03-18 07:55:23,147] [INFO] Running command: fastANI --query /var/lib/cwl/stge907bd51-b907-41dd-8fd9-38d589debdc6/OceanDNA-b112.fa --refList OceanDNA-b112/target_genomes_gtdb.txt --output OceanDNA-b112/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:55:30,443] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:30,450] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:55:30,451] [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_016190945.1	s__Gp6-AA40 sp016190945	77.648	112	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871375.1	s__Gp6-AA40 sp016871375	76.7613	112	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016210845.1	s__Gp6-AA40 sp016210845	76.7366	92	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016184455.1	s__Gp6-AA40 sp016184455	76.6769	120	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213695.1	s__Gp6-AA40 sp016213695	76.6001	126	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767525.1	s__Gp6-AA40 sp001767525	76.5468	133	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.96	99.96	0.95	0.95	2	-
GCA_001767195.1	s__Gp6-AA40 sp001767195	76.5057	128	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.78	99.78	0.93	0.93	2	-
GCA_013140775.1	s__Gp6-AA40 sp013140775	76.2214	86	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222635.1	s__Gp6-AA40 sp003222635	76.0626	90	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	98.94	98.94	0.87	0.87	2	-
GCA_017883165.1	s__JADGOC01 sp017883165	75.8321	60	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768615.1	s__12-FULL-67-14b sp001768615	75.6982	51	622	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:55:30,451] [INFO] GTDB search result was written to OceanDNA-b112/result_gtdb.tsv
[2023-03-18 07:55:30,451] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:55:30,452] [INFO] DFAST_QC result json was written to OceanDNA-b112/dqc_result.json
[2023-03-18 07:55:30,452] [INFO] DFAST_QC completed!
[2023-03-18 07:55:30,452] [INFO] Total running time: 0h1m1s