[2023-03-19 04:52:18,026] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:52:18,040] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:52:18,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg802f2682-3db6-49ef-a95f-a602adaf20b1/dqc_reference
[2023-03-19 04:52:19,130] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:52:19,130] [INFO] Task started: Prodigal
[2023-03-19 04:52:19,130] [INFO] Running command: cat /var/lib/cwl/stg856d45b8-c08e-4cf8-9ec9-676abf2c3396/OceanDNA-b23108.fa | prodigal -d OceanDNA-b23108/cds.fna -a OceanDNA-b23108/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:52:36,257] [INFO] Task succeeded: Prodigal
[2023-03-19 04:52:36,257] [INFO] Task started: HMMsearch
[2023-03-19 04:52:36,257] [INFO] Running command: hmmsearch --tblout OceanDNA-b23108/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg802f2682-3db6-49ef-a95f-a602adaf20b1/dqc_reference/reference_markers.hmm OceanDNA-b23108/protein.faa > /dev/null
[2023-03-19 04:52:36,443] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:52:36,444] [INFO] Found 6/6 markers.
[2023-03-19 04:52:36,463] [INFO] Query marker FASTA was written to OceanDNA-b23108/markers.fasta
[2023-03-19 04:52:36,464] [INFO] Task started: Blastn
[2023-03-19 04:52:36,464] [INFO] Running command: blastn -query OceanDNA-b23108/markers.fasta -db /var/lib/cwl/stg802f2682-3db6-49ef-a95f-a602adaf20b1/dqc_reference/reference_markers.fasta -out OceanDNA-b23108/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:52:37,063] [INFO] Task succeeded: Blastn
[2023-03-19 04:52:37,064] [INFO] Selected 20 target genomes.
[2023-03-19 04:52:37,064] [INFO] Target genome list was writen to OceanDNA-b23108/target_genomes.txt
[2023-03-19 04:52:37,104] [INFO] Task started: fastANI
[2023-03-19 04:52:37,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg856d45b8-c08e-4cf8-9ec9-676abf2c3396/OceanDNA-b23108.fa --refList OceanDNA-b23108/target_genomes.txt --output OceanDNA-b23108/fastani_result.tsv --threads 1
[2023-03-19 04:52:50,485] [INFO] Task succeeded: fastANI
[2023-03-19 04:52:50,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg802f2682-3db6-49ef-a95f-a602adaf20b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:52:50,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg802f2682-3db6-49ef-a95f-a602adaf20b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:52:50,486] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:52:50,486] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:52:50,486] [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 04:52:50,487] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23108/tc_result.tsv
[2023-03-19 04:52:50,489] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:52:50,489] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:52:50,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg802f2682-3db6-49ef-a95f-a602adaf20b1/dqc_reference/checkm_data
[2023-03-19 04:52:50,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:52:50,497] [INFO] Task started: CheckM
[2023-03-19 04:52:50,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23108/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23108/checkm_input OceanDNA-b23108/checkm_result
[2023-03-19 04:53:36,307] [INFO] Task succeeded: CheckM
[2023-03-19 04:53:36,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:53:36,311] [INFO] ===== Completeness check finished =====
[2023-03-19 04:53:36,312] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:53:36,312] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23108/markers.fasta)
[2023-03-19 04:53:36,313] [INFO] Task started: Blastn
[2023-03-19 04:53:36,313] [INFO] Running command: blastn -query OceanDNA-b23108/markers.fasta -db /var/lib/cwl/stg802f2682-3db6-49ef-a95f-a602adaf20b1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23108/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:53:37,042] [INFO] Task succeeded: Blastn
[2023-03-19 04:53:37,044] [INFO] Selected 8 target genomes.
[2023-03-19 04:53:37,044] [INFO] Target genome list was writen to OceanDNA-b23108/target_genomes_gtdb.txt
[2023-03-19 04:53:37,054] [INFO] Task started: fastANI
[2023-03-19 04:53:37,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg856d45b8-c08e-4cf8-9ec9-676abf2c3396/OceanDNA-b23108.fa --refList OceanDNA-b23108/target_genomes_gtdb.txt --output OceanDNA-b23108/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:53:42,045] [INFO] Task succeeded: fastANI
[2023-03-19 04:53:42,050] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:53:42,050] [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_018694835.1	s__QNYK01 sp018694835	99.7608	823	894	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	99.80	99.78	0.93	0.92	8	conclusive
GCA_012960845.1	s__QNYK01 sp012960845	94.4266	784	894	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	99.73	99.73	0.93	0.93	2	-
GCA_014240375.1	s__QNYK01 sp014240375	93.3412	847	894	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003973385.1	s__QNYK01 sp003973385	79.4611	382	894	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	99.67	99.67	0.93	0.93	2	-
GCA_002711105.1	s__UBA1146 sp002711105	77.6889	200	894	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA1146	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911165.1	s__UBA12191 sp013911165	76.4689	72	894	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269595.1	s__UBA12191 sp012269595	76.4529	84	894	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	99.68	99.68	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:53:42,051] [INFO] GTDB search result was written to OceanDNA-b23108/result_gtdb.tsv
[2023-03-19 04:53:42,052] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:53:42,053] [INFO] DFAST_QC result json was written to OceanDNA-b23108/dqc_result.json
[2023-03-19 04:53:42,053] [INFO] DFAST_QC completed!
[2023-03-19 04:53:42,053] [INFO] Total running time: 0h1m24s