[2023-03-16 06:33:31,996] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:33:31,996] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:33:31,996] [INFO] DQC Reference Directory: /var/lib/cwl/stgde164144-eab9-46d7-b2fd-b832f423e712/dqc_reference
[2023-03-16 06:33:33,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:33:33,083] [INFO] Task started: Prodigal
[2023-03-16 06:33:33,083] [INFO] Running command: cat /var/lib/cwl/stgf1aa3112-0897-4c05-9a15-600f49a6a538/OceanDNA-b23102.fa | prodigal -d OceanDNA-b23102/cds.fna -a OceanDNA-b23102/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:33:48,932] [INFO] Task succeeded: Prodigal
[2023-03-16 06:33:48,932] [INFO] Task started: HMMsearch
[2023-03-16 06:33:48,932] [INFO] Running command: hmmsearch --tblout OceanDNA-b23102/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde164144-eab9-46d7-b2fd-b832f423e712/dqc_reference/reference_markers.hmm OceanDNA-b23102/protein.faa > /dev/null
[2023-03-16 06:33:49,097] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:33:49,098] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf1aa3112-0897-4c05-9a15-600f49a6a538/OceanDNA-b23102.fa]
[2023-03-16 06:33:49,117] [INFO] Query marker FASTA was written to OceanDNA-b23102/markers.fasta
[2023-03-16 06:33:49,118] [INFO] Task started: Blastn
[2023-03-16 06:33:49,119] [INFO] Running command: blastn -query OceanDNA-b23102/markers.fasta -db /var/lib/cwl/stgde164144-eab9-46d7-b2fd-b832f423e712/dqc_reference/reference_markers.fasta -out OceanDNA-b23102/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:33:49,617] [INFO] Task succeeded: Blastn
[2023-03-16 06:33:49,618] [INFO] Selected 15 target genomes.
[2023-03-16 06:33:49,618] [INFO] Target genome list was writen to OceanDNA-b23102/target_genomes.txt
[2023-03-16 06:33:49,628] [INFO] Task started: fastANI
[2023-03-16 06:33:49,628] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1aa3112-0897-4c05-9a15-600f49a6a538/OceanDNA-b23102.fa --refList OceanDNA-b23102/target_genomes.txt --output OceanDNA-b23102/fastani_result.tsv --threads 1
[2023-03-16 06:34:02,638] [INFO] Task succeeded: fastANI
[2023-03-16 06:34:02,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde164144-eab9-46d7-b2fd-b832f423e712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:34:02,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde164144-eab9-46d7-b2fd-b832f423e712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:34:02,639] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:34:02,639] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:34:02,639] [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
--------------------------------------------------------------------------------
[2023-03-16 06:34:02,639] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23102/tc_result.tsv
[2023-03-16 06:34:02,640] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:34:02,640] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:34:02,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde164144-eab9-46d7-b2fd-b832f423e712/dqc_reference/checkm_data
[2023-03-16 06:34:02,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:34:02,711] [INFO] Task started: CheckM
[2023-03-16 06:34:02,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23102/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23102/checkm_input OceanDNA-b23102/checkm_result
[2023-03-16 06:34:45,141] [INFO] Task succeeded: CheckM
[2023-03-16 06:34:45,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:34:45,143] [INFO] ===== Completeness check finished =====
[2023-03-16 06:34:45,143] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:34:45,143] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23102/markers.fasta)
[2023-03-16 06:34:45,144] [INFO] Task started: Blastn
[2023-03-16 06:34:45,144] [INFO] Running command: blastn -query OceanDNA-b23102/markers.fasta -db /var/lib/cwl/stgde164144-eab9-46d7-b2fd-b832f423e712/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23102/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:34:45,848] [INFO] Task succeeded: Blastn
[2023-03-16 06:34:45,849] [INFO] Selected 8 target genomes.
[2023-03-16 06:34:45,849] [INFO] Target genome list was writen to OceanDNA-b23102/target_genomes_gtdb.txt
[2023-03-16 06:34:45,853] [INFO] Task started: fastANI
[2023-03-16 06:34:45,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1aa3112-0897-4c05-9a15-600f49a6a538/OceanDNA-b23102.fa --refList OceanDNA-b23102/target_genomes_gtdb.txt --output OceanDNA-b23102/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:34:51,456] [INFO] Task succeeded: fastANI
[2023-03-16 06:34:51,461] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:34:51,461] [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_002684655.1	s__GCA-2684655 sp002684655	99.387	346	360	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__GCA-2684655	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011051855.1	s__GCA-2684655 sp011051855	78.364	112	360	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__GCA-2684655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872675.1	s__UBA2386 sp016872675	77.9362	119	360	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794035.1	s__JAEUHS01 sp016794035	77.6894	126	360	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794425.1	s__JAEUHS01 sp016794425	77.5947	124	360	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794485.1	s__UBA2386 sp016794485	77.3308	112	360	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793305.1	s__UBA2386 sp016793305	76.9724	98	360	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873195.1	s__VGXW01 sp016873195	76.8893	98	360	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:34:51,461] [INFO] GTDB search result was written to OceanDNA-b23102/result_gtdb.tsv
[2023-03-16 06:34:51,462] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:34:51,462] [INFO] DFAST_QC result json was written to OceanDNA-b23102/dqc_result.json
[2023-03-16 06:34:51,462] [INFO] DFAST_QC completed!
[2023-03-16 06:34:51,462] [INFO] Total running time: 0h1m19s