[2023-03-15 06:50:51,574] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:50:51,585] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:50:51,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e11697b-91f2-4c20-abce-f3758b6c8216/dqc_reference
[2023-03-15 06:50:53,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:50:53,468] [INFO] Task started: Prodigal
[2023-03-15 06:50:53,469] [INFO] Running command: cat /var/lib/cwl/stg155de700-ae3a-4945-ab9d-33995b3c7f91/OceanDNA-b19919.fa | prodigal -d OceanDNA-b19919/cds.fna -a OceanDNA-b19919/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:51:01,589] [INFO] Task succeeded: Prodigal
[2023-03-15 06:51:01,589] [INFO] Task started: HMMsearch
[2023-03-15 06:51:01,589] [INFO] Running command: hmmsearch --tblout OceanDNA-b19919/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e11697b-91f2-4c20-abce-f3758b6c8216/dqc_reference/reference_markers.hmm OceanDNA-b19919/protein.faa > /dev/null
[2023-03-15 06:51:01,750] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:51:01,751] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg155de700-ae3a-4945-ab9d-33995b3c7f91/OceanDNA-b19919.fa]
[2023-03-15 06:51:01,862] [INFO] Query marker FASTA was written to OceanDNA-b19919/markers.fasta
[2023-03-15 06:51:01,864] [INFO] Task started: Blastn
[2023-03-15 06:51:01,864] [INFO] Running command: blastn -query OceanDNA-b19919/markers.fasta -db /var/lib/cwl/stg8e11697b-91f2-4c20-abce-f3758b6c8216/dqc_reference/reference_markers.fasta -out OceanDNA-b19919/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:51:02,378] [INFO] Task succeeded: Blastn
[2023-03-15 06:51:02,415] [INFO] Selected 20 target genomes.
[2023-03-15 06:51:02,416] [INFO] Target genome list was writen to OceanDNA-b19919/target_genomes.txt
[2023-03-15 06:51:02,468] [INFO] Task started: fastANI
[2023-03-15 06:51:02,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg155de700-ae3a-4945-ab9d-33995b3c7f91/OceanDNA-b19919.fa --refList OceanDNA-b19919/target_genomes.txt --output OceanDNA-b19919/fastani_result.tsv --threads 1
[2023-03-15 06:51:13,367] [INFO] Task succeeded: fastANI
[2023-03-15 06:51:13,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e11697b-91f2-4c20-abce-f3758b6c8216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:51:13,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e11697b-91f2-4c20-abce-f3758b6c8216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:51:13,368] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:51:13,368] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:51:13,368] [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 06:51:13,373] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19919/tc_result.tsv
[2023-03-15 06:51:13,382] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:51:13,382] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:51:13,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e11697b-91f2-4c20-abce-f3758b6c8216/dqc_reference/checkm_data
[2023-03-15 06:51:13,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:51:13,522] [INFO] Task started: CheckM
[2023-03-15 06:51:13,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19919/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19919/checkm_input OceanDNA-b19919/checkm_result
[2023-03-15 06:51:38,785] [INFO] Task succeeded: CheckM
[2023-03-15 06:51:38,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 06:51:39,082] [INFO] ===== Completeness check finished =====
[2023-03-15 06:51:39,082] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:51:39,082] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19919/markers.fasta)
[2023-03-15 06:51:39,083] [INFO] Task started: Blastn
[2023-03-15 06:51:39,083] [INFO] Running command: blastn -query OceanDNA-b19919/markers.fasta -db /var/lib/cwl/stg8e11697b-91f2-4c20-abce-f3758b6c8216/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19919/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:51:39,746] [INFO] Task succeeded: Blastn
[2023-03-15 06:51:39,747] [INFO] Selected 20 target genomes.
[2023-03-15 06:51:39,747] [INFO] Target genome list was writen to OceanDNA-b19919/target_genomes_gtdb.txt
[2023-03-15 06:51:39,871] [INFO] Task started: fastANI
[2023-03-15 06:51:39,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg155de700-ae3a-4945-ab9d-33995b3c7f91/OceanDNA-b19919.fa --refList OceanDNA-b19919/target_genomes_gtdb.txt --output OceanDNA-b19919/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:51:46,561] [INFO] Task succeeded: fastANI
[2023-03-15 06:51:46,564] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:51:46,565] [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_018692355.1	s__GCA-2722105 sp018692355	88.1485	320	492	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.23	99.02	0.79	0.73	14	-
GCA_015658495.1	s__GCA-2722105 sp015658495	79.3622	147	492	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674095.1	s__GCA-2722105 sp018674095	78.9384	149	492	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.41	99.30	0.88	0.82	13	-
GCA_018649625.1	s__GCA-2722105 sp018649625	76.6891	115	492	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.96	99.90	0.93	0.85	15	-
--------------------------------------------------------------------------------
[2023-03-15 06:51:46,565] [INFO] GTDB search result was written to OceanDNA-b19919/result_gtdb.tsv
[2023-03-15 06:51:46,565] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:51:46,566] [INFO] DFAST_QC result json was written to OceanDNA-b19919/dqc_result.json
[2023-03-15 06:51:46,566] [INFO] DFAST_QC completed!
[2023-03-15 06:51:46,566] [INFO] Total running time: 0h0m55s