[2023-03-15 11:51:17,347] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg356e7cc7-0bf8-43eb-8b54-bdeadcbc8c28/dqc_reference
[2023-03-15 11:51:18,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,950] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,951] [INFO] Running command: cat /var/lib/cwl/stgbf9c2a65-9dee-4799-977e-e95317adaa58/OceanDNA-b15167.fa | prodigal -d OceanDNA-b15167/cds.fna -a OceanDNA-b15167/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:27,305] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:27,305] [INFO] Task started: HMMsearch
[2023-03-15 11:51:27,305] [INFO] Running command: hmmsearch --tblout OceanDNA-b15167/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg356e7cc7-0bf8-43eb-8b54-bdeadcbc8c28/dqc_reference/reference_markers.hmm OceanDNA-b15167/protein.faa > /dev/null
[2023-03-15 11:51:27,455] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:27,455] [INFO] Found 6/6 markers.
[2023-03-15 11:51:27,470] [INFO] Query marker FASTA was written to OceanDNA-b15167/markers.fasta
[2023-03-15 11:51:27,471] [INFO] Task started: Blastn
[2023-03-15 11:51:27,471] [INFO] Running command: blastn -query OceanDNA-b15167/markers.fasta -db /var/lib/cwl/stg356e7cc7-0bf8-43eb-8b54-bdeadcbc8c28/dqc_reference/reference_markers.fasta -out OceanDNA-b15167/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:28,026] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:28,027] [INFO] Selected 25 target genomes.
[2023-03-15 11:51:28,028] [INFO] Target genome list was writen to OceanDNA-b15167/target_genomes.txt
[2023-03-15 11:51:28,044] [INFO] Task started: fastANI
[2023-03-15 11:51:28,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf9c2a65-9dee-4799-977e-e95317adaa58/OceanDNA-b15167.fa --refList OceanDNA-b15167/target_genomes.txt --output OceanDNA-b15167/fastani_result.tsv --threads 1
[2023-03-15 11:51:44,995] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:44,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg356e7cc7-0bf8-43eb-8b54-bdeadcbc8c28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:44,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg356e7cc7-0bf8-43eb-8b54-bdeadcbc8c28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:45,000] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:45,000] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:51:45,000] [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
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	74.9163	72	409	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	74.7353	50	409	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	74.6956	58	409	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:51:45,000] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15167/tc_result.tsv
[2023-03-15 11:51:45,000] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:45,000] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:45,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg356e7cc7-0bf8-43eb-8b54-bdeadcbc8c28/dqc_reference/checkm_data
[2023-03-15 11:51:45,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:45,005] [INFO] Task started: CheckM
[2023-03-15 11:51:45,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15167/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15167/checkm_input OceanDNA-b15167/checkm_result
[2023-03-15 11:52:10,562] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:10,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:10,564] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:10,565] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:10,565] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15167/markers.fasta)
[2023-03-15 11:52:10,566] [INFO] Task started: Blastn
[2023-03-15 11:52:10,566] [INFO] Running command: blastn -query OceanDNA-b15167/markers.fasta -db /var/lib/cwl/stg356e7cc7-0bf8-43eb-8b54-bdeadcbc8c28/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15167/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:11,437] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:11,438] [INFO] Selected 14 target genomes.
[2023-03-15 11:52:11,438] [INFO] Target genome list was writen to OceanDNA-b15167/target_genomes_gtdb.txt
[2023-03-15 11:52:11,455] [INFO] Task started: fastANI
[2023-03-15 11:52:11,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf9c2a65-9dee-4799-977e-e95317adaa58/OceanDNA-b15167.fa --refList OceanDNA-b15167/target_genomes_gtdb.txt --output OceanDNA-b15167/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:16,376] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:16,384] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:52:16,385] [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_009692705.1	s__SHYR01 sp009692705	78.0272	73	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SHYR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009839925.1	s__VXMT01 sp009839925	77.4339	111	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840965.1	s__VXMT01 sp009840965	77.3602	108	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	96.91	96.91	0.81	0.81	2	-
GCA_016866055.1	s__VGNK01 sp016866055	77.2453	131	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VGNK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840945.1	s__VXMT01 sp009840945	77.232	104	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837285.1	s__VXMT01 sp009837285	77.0321	91	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	95.62	95.50	0.87	0.82	3	-
GCA_016875695.1	s__SHYP01 sp016875695	76.9832	66	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SHYP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379925.1	s__WHSU01 sp009379925	76.8459	101	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__WHSU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840675.1	s__W-Chloroflexi-9 sp002840675	76.7945	73	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__W-Chloroflexi-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692685.1	s__RBC038 sp009692685	76.6923	66	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__RBC038	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692725.1	s__SHYP01 sp009692725	76.6635	54	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SHYP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875635.1	s__SURF-43 sp016875635	76.5371	67	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SURF-43	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296805.1	s__SURF-43 sp004296805	76.1353	53	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SURF-43	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:16,385] [INFO] GTDB search result was written to OceanDNA-b15167/result_gtdb.tsv
[2023-03-15 11:52:16,385] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:16,386] [INFO] DFAST_QC result json was written to OceanDNA-b15167/dqc_result.json
[2023-03-15 11:52:16,386] [INFO] DFAST_QC completed!
[2023-03-15 11:52:16,386] [INFO] Total running time: 0h0m59s