[2023-03-16 00:33:46,601] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:33:46,601] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:33:46,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg72ee75d2-1a86-469b-a7c3-b470b30ea9f6/dqc_reference
[2023-03-16 00:33:47,718] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:33:47,718] [INFO] Task started: Prodigal
[2023-03-16 00:33:47,718] [INFO] Running command: cat /var/lib/cwl/stg50128142-8730-4760-84c8-c4a540d9e774/OceanDNA-b15088.fa | prodigal -d OceanDNA-b15088/cds.fna -a OceanDNA-b15088/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:34:02,621] [INFO] Task succeeded: Prodigal
[2023-03-16 00:34:02,621] [INFO] Task started: HMMsearch
[2023-03-16 00:34:02,622] [INFO] Running command: hmmsearch --tblout OceanDNA-b15088/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72ee75d2-1a86-469b-a7c3-b470b30ea9f6/dqc_reference/reference_markers.hmm OceanDNA-b15088/protein.faa > /dev/null
[2023-03-16 00:34:02,796] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:34:02,796] [INFO] Found 6/6 markers.
[2023-03-16 00:34:02,813] [INFO] Query marker FASTA was written to OceanDNA-b15088/markers.fasta
[2023-03-16 00:34:02,815] [INFO] Task started: Blastn
[2023-03-16 00:34:02,815] [INFO] Running command: blastn -query OceanDNA-b15088/markers.fasta -db /var/lib/cwl/stg72ee75d2-1a86-469b-a7c3-b470b30ea9f6/dqc_reference/reference_markers.fasta -out OceanDNA-b15088/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:34:03,351] [INFO] Task succeeded: Blastn
[2023-03-16 00:34:03,352] [INFO] Selected 10 target genomes.
[2023-03-16 00:34:03,352] [INFO] Target genome list was writen to OceanDNA-b15088/target_genomes.txt
[2023-03-16 00:34:03,470] [INFO] Task started: fastANI
[2023-03-16 00:34:03,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg50128142-8730-4760-84c8-c4a540d9e774/OceanDNA-b15088.fa --refList OceanDNA-b15088/target_genomes.txt --output OceanDNA-b15088/fastani_result.tsv --threads 1
[2023-03-16 00:34:10,286] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:10,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72ee75d2-1a86-469b-a7c3-b470b30ea9f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:34:10,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72ee75d2-1a86-469b-a7c3-b470b30ea9f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:34:10,287] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:34:10,287] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:34:10,287] [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 00:34:10,287] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15088/tc_result.tsv
[2023-03-16 00:34:10,287] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:34:10,287] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:34:10,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72ee75d2-1a86-469b-a7c3-b470b30ea9f6/dqc_reference/checkm_data
[2023-03-16 00:34:10,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:34:10,294] [INFO] Task started: CheckM
[2023-03-16 00:34:10,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15088/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15088/checkm_input OceanDNA-b15088/checkm_result
[2023-03-16 00:34:50,552] [INFO] Task succeeded: CheckM
[2023-03-16 00:34:50,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 00:34:50,570] [INFO] ===== Completeness check finished =====
[2023-03-16 00:34:50,570] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:34:50,570] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15088/markers.fasta)
[2023-03-16 00:34:50,572] [INFO] Task started: Blastn
[2023-03-16 00:34:50,572] [INFO] Running command: blastn -query OceanDNA-b15088/markers.fasta -db /var/lib/cwl/stg72ee75d2-1a86-469b-a7c3-b470b30ea9f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15088/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:34:51,381] [INFO] Task succeeded: Blastn
[2023-03-16 00:34:51,382] [INFO] Selected 13 target genomes.
[2023-03-16 00:34:51,382] [INFO] Target genome list was writen to OceanDNA-b15088/target_genomes_gtdb.txt
[2023-03-16 00:34:51,400] [INFO] Task started: fastANI
[2023-03-16 00:34:51,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg50128142-8730-4760-84c8-c4a540d9e774/OceanDNA-b15088.fa --refList OceanDNA-b15088/target_genomes_gtdb.txt --output OceanDNA-b15088/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:34:58,661] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:58,664] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:34:58,664] [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_014239685.1	s__GCA-2730555 sp014239685	83.006	445	809	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730555.1	s__GCA-2730555 sp002730555	79.7416	486	809	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.68	99.68	0.93	0.93	2	-
GCA_018650185.1	s__GCA-2730555 sp018650185	78.6171	381	809	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.67	99.66	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-16 00:34:58,667] [INFO] GTDB search result was written to OceanDNA-b15088/result_gtdb.tsv
[2023-03-16 00:34:58,667] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:34:58,667] [INFO] DFAST_QC result json was written to OceanDNA-b15088/dqc_result.json
[2023-03-16 00:34:58,668] [INFO] DFAST_QC completed!
[2023-03-16 00:34:58,668] [INFO] Total running time: 0h1m12s