[2023-03-17 08:04:06,981] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:04:06,981] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:04:06,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg882ca3eb-70a6-406f-81df-c0a8bdbd2ce3/dqc_reference
[2023-03-17 08:04:08,770] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:04:08,770] [INFO] Task started: Prodigal
[2023-03-17 08:04:08,770] [INFO] Running command: cat /var/lib/cwl/stg39ee4569-ddbd-4a25-aec5-32e87fc4a4d0/OceanDNA-b20148.fa | prodigal -d OceanDNA-b20148/cds.fna -a OceanDNA-b20148/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:04:17,889] [INFO] Task succeeded: Prodigal
[2023-03-17 08:04:17,890] [INFO] Task started: HMMsearch
[2023-03-17 08:04:17,890] [INFO] Running command: hmmsearch --tblout OceanDNA-b20148/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg882ca3eb-70a6-406f-81df-c0a8bdbd2ce3/dqc_reference/reference_markers.hmm OceanDNA-b20148/protein.faa > /dev/null
[2023-03-17 08:04:18,050] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:04:18,051] [INFO] Found 6/6 markers.
[2023-03-17 08:04:18,064] [INFO] Query marker FASTA was written to OceanDNA-b20148/markers.fasta
[2023-03-17 08:04:18,064] [INFO] Task started: Blastn
[2023-03-17 08:04:18,064] [INFO] Running command: blastn -query OceanDNA-b20148/markers.fasta -db /var/lib/cwl/stg882ca3eb-70a6-406f-81df-c0a8bdbd2ce3/dqc_reference/reference_markers.fasta -out OceanDNA-b20148/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:04:18,563] [INFO] Task succeeded: Blastn
[2023-03-17 08:04:18,564] [INFO] Selected 17 target genomes.
[2023-03-17 08:04:18,564] [INFO] Target genome list was writen to OceanDNA-b20148/target_genomes.txt
[2023-03-17 08:04:18,573] [INFO] Task started: fastANI
[2023-03-17 08:04:18,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ee4569-ddbd-4a25-aec5-32e87fc4a4d0/OceanDNA-b20148.fa --refList OceanDNA-b20148/target_genomes.txt --output OceanDNA-b20148/fastani_result.tsv --threads 1
[2023-03-17 08:04:25,519] [INFO] Task succeeded: fastANI
[2023-03-17 08:04:25,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg882ca3eb-70a6-406f-81df-c0a8bdbd2ce3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:04:25,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg882ca3eb-70a6-406f-81df-c0a8bdbd2ce3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:04:25,519] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:04:25,519] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:04:25,519] [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
--------------------------------------------------------------------------------
[2023-03-17 08:04:25,520] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20148/tc_result.tsv
[2023-03-17 08:04:25,520] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:04:25,520] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:04:25,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg882ca3eb-70a6-406f-81df-c0a8bdbd2ce3/dqc_reference/checkm_data
[2023-03-17 08:04:25,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:04:25,564] [INFO] Task started: CheckM
[2023-03-17 08:04:25,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20148/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20148/checkm_input OceanDNA-b20148/checkm_result
[2023-03-17 08:04:52,781] [INFO] Task succeeded: CheckM
[2023-03-17 08:04:52,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 08:04:52,783] [INFO] ===== Completeness check finished =====
[2023-03-17 08:04:52,784] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:04:52,784] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20148/markers.fasta)
[2023-03-17 08:04:52,784] [INFO] Task started: Blastn
[2023-03-17 08:04:52,784] [INFO] Running command: blastn -query OceanDNA-b20148/markers.fasta -db /var/lib/cwl/stg882ca3eb-70a6-406f-81df-c0a8bdbd2ce3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20148/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:04:53,471] [INFO] Task succeeded: Blastn
[2023-03-17 08:04:53,472] [INFO] Selected 19 target genomes.
[2023-03-17 08:04:53,472] [INFO] Target genome list was writen to OceanDNA-b20148/target_genomes_gtdb.txt
[2023-03-17 08:04:54,046] [INFO] Task started: fastANI
[2023-03-17 08:04:54,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ee4569-ddbd-4a25-aec5-32e87fc4a4d0/OceanDNA-b20148.fa --refList OceanDNA-b20148/target_genomes_gtdb.txt --output OceanDNA-b20148/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:04:59,985] [INFO] Task succeeded: fastANI
[2023-03-17 08:04:59,989] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:04:59,989] [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_018645565.1	s__TMED80 sp018645565	99.3149	477	601	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	99.41	99.35	0.85	0.81	6	conclusive
GCA_905478065.1	s__TMED80 sp905478065	92.4099	469	601	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559415.1	s__TMED80 sp902559415	78.5891	136	601	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004321745.1	s__TMED80 sp002170405	77.5114	159	601	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	99.32	99.32	0.73	0.73	2	-
GCA_002169695.1	s__TMED80 sp002169695	76.5482	65	601	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:04:59,990] [INFO] GTDB search result was written to OceanDNA-b20148/result_gtdb.tsv
[2023-03-17 08:04:59,990] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:04:59,990] [INFO] DFAST_QC result json was written to OceanDNA-b20148/dqc_result.json
[2023-03-17 08:04:59,990] [INFO] DFAST_QC completed!
[2023-03-17 08:04:59,991] [INFO] Total running time: 0h0m53s