[2023-03-19 00:54:54,800] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:54:54,800] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:54:54,801] [INFO] DQC Reference Directory: /var/lib/cwl/stgba0623b0-61b5-4969-8586-fd6925450f81/dqc_reference
[2023-03-19 00:54:55,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:54:55,891] [INFO] Task started: Prodigal
[2023-03-19 00:54:55,892] [INFO] Running command: cat /var/lib/cwl/stg453914e8-2df4-4970-a1fc-3f8f35cc8ef6/OceanDNA-b20036.fa | prodigal -d OceanDNA-b20036/cds.fna -a OceanDNA-b20036/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:55:07,298] [INFO] Task succeeded: Prodigal
[2023-03-19 00:55:07,299] [INFO] Task started: HMMsearch
[2023-03-19 00:55:07,299] [INFO] Running command: hmmsearch --tblout OceanDNA-b20036/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba0623b0-61b5-4969-8586-fd6925450f81/dqc_reference/reference_markers.hmm OceanDNA-b20036/protein.faa > /dev/null
[2023-03-19 00:55:07,470] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:55:07,471] [INFO] Found 6/6 markers.
[2023-03-19 00:55:07,486] [INFO] Query marker FASTA was written to OceanDNA-b20036/markers.fasta
[2023-03-19 00:55:07,487] [INFO] Task started: Blastn
[2023-03-19 00:55:07,487] [INFO] Running command: blastn -query OceanDNA-b20036/markers.fasta -db /var/lib/cwl/stgba0623b0-61b5-4969-8586-fd6925450f81/dqc_reference/reference_markers.fasta -out OceanDNA-b20036/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:55:07,995] [INFO] Task succeeded: Blastn
[2023-03-19 00:55:07,996] [INFO] Selected 23 target genomes.
[2023-03-19 00:55:07,996] [INFO] Target genome list was writen to OceanDNA-b20036/target_genomes.txt
[2023-03-19 00:55:08,009] [INFO] Task started: fastANI
[2023-03-19 00:55:08,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg453914e8-2df4-4970-a1fc-3f8f35cc8ef6/OceanDNA-b20036.fa --refList OceanDNA-b20036/target_genomes.txt --output OceanDNA-b20036/fastani_result.tsv --threads 1
[2023-03-19 00:55:17,267] [INFO] Task succeeded: fastANI
[2023-03-19 00:55:17,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba0623b0-61b5-4969-8586-fd6925450f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:55:17,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba0623b0-61b5-4969-8586-fd6925450f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:55:17,268] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:55:17,268] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:55:17,268] [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
--------------------------------------------------------------------------------
[2023-03-19 00:55:17,269] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20036/tc_result.tsv
[2023-03-19 00:55:17,269] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:55:17,269] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:55:17,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba0623b0-61b5-4969-8586-fd6925450f81/dqc_reference/checkm_data
[2023-03-19 00:55:17,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:55:17,301] [INFO] Task started: CheckM
[2023-03-19 00:55:17,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20036/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20036/checkm_input OceanDNA-b20036/checkm_result
[2023-03-19 00:55:49,741] [INFO] Task succeeded: CheckM
[2023-03-19 00:55:49,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:55:49,857] [INFO] ===== Completeness check finished =====
[2023-03-19 00:55:49,857] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:55:49,857] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20036/markers.fasta)
[2023-03-19 00:55:49,858] [INFO] Task started: Blastn
[2023-03-19 00:55:49,858] [INFO] Running command: blastn -query OceanDNA-b20036/markers.fasta -db /var/lib/cwl/stgba0623b0-61b5-4969-8586-fd6925450f81/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20036/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:55:50,563] [INFO] Task succeeded: Blastn
[2023-03-19 00:55:50,565] [INFO] Selected 24 target genomes.
[2023-03-19 00:55:50,565] [INFO] Target genome list was writen to OceanDNA-b20036/target_genomes_gtdb.txt
[2023-03-19 00:55:50,595] [INFO] Task started: fastANI
[2023-03-19 00:55:50,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg453914e8-2df4-4970-a1fc-3f8f35cc8ef6/OceanDNA-b20036.fa --refList OceanDNA-b20036/target_genomes_gtdb.txt --output OceanDNA-b20036/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:55:58,055] [INFO] Task succeeded: fastANI
[2023-03-19 00:55:58,059] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:55:58,059] [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_002722105.1	s__GCA-2722105 sp002722105	97.8092	556	726	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015658495.1	s__GCA-2722105 sp015658495	76.6708	50	726	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	76.5387	109	726	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_002718285.1	s__UBA2134 sp002718285	76.1784	54	726	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__UBA2134	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:55:58,060] [INFO] GTDB search result was written to OceanDNA-b20036/result_gtdb.tsv
[2023-03-19 00:55:58,060] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:55:58,062] [INFO] DFAST_QC result json was written to OceanDNA-b20036/dqc_result.json
[2023-03-19 00:55:58,062] [INFO] DFAST_QC completed!
[2023-03-19 00:55:58,062] [INFO] Total running time: 0h1m3s