[2023-03-18 20:55:49,217] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:55:49,217] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:55:49,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c870d99-bc16-414b-9264-42ac1ad03309/dqc_reference
[2023-03-18 20:55:50,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:55:50,317] [INFO] Task started: Prodigal
[2023-03-18 20:55:50,317] [INFO] Running command: cat /var/lib/cwl/stg66375652-13b0-4e08-9ee4-ab7cd3dd3530/OceanDNA-b23093.fa | prodigal -d OceanDNA-b23093/cds.fna -a OceanDNA-b23093/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:56:36,969] [INFO] Task succeeded: Prodigal
[2023-03-18 20:56:36,969] [INFO] Task started: HMMsearch
[2023-03-18 20:56:36,969] [INFO] Running command: hmmsearch --tblout OceanDNA-b23093/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c870d99-bc16-414b-9264-42ac1ad03309/dqc_reference/reference_markers.hmm OceanDNA-b23093/protein.faa > /dev/null
[2023-03-18 20:56:37,300] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:56:37,300] [INFO] Found 6/6 markers.
[2023-03-18 20:56:37,341] [INFO] Query marker FASTA was written to OceanDNA-b23093/markers.fasta
[2023-03-18 20:56:37,342] [INFO] Task started: Blastn
[2023-03-18 20:56:37,342] [INFO] Running command: blastn -query OceanDNA-b23093/markers.fasta -db /var/lib/cwl/stg9c870d99-bc16-414b-9264-42ac1ad03309/dqc_reference/reference_markers.fasta -out OceanDNA-b23093/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:41,227] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:41,228] [INFO] Selected 25 target genomes.
[2023-03-18 20:56:41,228] [INFO] Target genome list was writen to OceanDNA-b23093/target_genomes.txt
[2023-03-18 20:56:41,239] [INFO] Task started: fastANI
[2023-03-18 20:56:41,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg66375652-13b0-4e08-9ee4-ab7cd3dd3530/OceanDNA-b23093.fa --refList OceanDNA-b23093/target_genomes.txt --output OceanDNA-b23093/fastani_result.tsv --threads 1
[2023-03-18 20:56:59,356] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:59,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c870d99-bc16-414b-9264-42ac1ad03309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:56:59,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c870d99-bc16-414b-9264-42ac1ad03309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:56:59,363] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:56:59,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:56:59,363] [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
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	74.9215	55	2348	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	74.8292	64	2348	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	74.7809	69	2348	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	74.7488	56	2348	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	74.7288	74	2348	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	74.708	98	2348	95	below_threshold
Bradyrhizobium oligotrophicum	strain=S58	GCA_000344805.1	44255	44255	type	True	74.6973	101	2348	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	74.5996	60	2348	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	74.5244	62	2348	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:56:59,363] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23093/tc_result.tsv
[2023-03-18 20:56:59,363] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:56:59,363] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:56:59,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c870d99-bc16-414b-9264-42ac1ad03309/dqc_reference/checkm_data
[2023-03-18 20:56:59,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:56:59,372] [INFO] Task started: CheckM
[2023-03-18 20:56:59,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23093/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23093/checkm_input OceanDNA-b23093/checkm_result
[2023-03-18 20:58:49,218] [INFO] Task succeeded: CheckM
[2023-03-18 20:58:49,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:58:49,223] [INFO] ===== Completeness check finished =====
[2023-03-18 20:58:49,223] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:58:49,223] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23093/markers.fasta)
[2023-03-18 20:58:49,223] [INFO] Task started: Blastn
[2023-03-18 20:58:49,223] [INFO] Running command: blastn -query OceanDNA-b23093/markers.fasta -db /var/lib/cwl/stg9c870d99-bc16-414b-9264-42ac1ad03309/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23093/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:58:50,047] [INFO] Task succeeded: Blastn
[2023-03-18 20:58:50,048] [INFO] Selected 12 target genomes.
[2023-03-18 20:58:50,048] [INFO] Target genome list was writen to OceanDNA-b23093/target_genomes_gtdb.txt
[2023-03-18 20:58:50,058] [INFO] Task started: fastANI
[2023-03-18 20:58:50,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg66375652-13b0-4e08-9ee4-ab7cd3dd3530/OceanDNA-b23093.fa --refList OceanDNA-b23093/target_genomes_gtdb.txt --output OceanDNA-b23093/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:59:00,316] [INFO] Task succeeded: fastANI
[2023-03-18 20:59:00,323] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:59:00,324] [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_011051855.1	s__GCA-2684655 sp011051855	78.505	477	2348	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_016794035.1	s__JAEUHS01 sp016794035	77.9834	512	2348	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793265.1	s__UBA2386 sp016793265	77.7977	468	2348	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794425.1	s__JAEUHS01 sp016794425	77.6295	532	2348	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872675.1	s__UBA2386 sp016872675	77.6004	445	2348	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684655.1	s__GCA-2684655 sp002684655	77.4884	373	2348	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_016794485.1	s__UBA2386 sp016794485	77.3491	498	2348	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	77.3185	413	2348	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343845.1	s__UBA2386 sp002343845	77.2112	368	2348	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794565.1	s__JAEUHS01 sp016794565	77.1472	390	2348	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005776475.1	s__UBA2386 sp005776475	77.0796	468	2348	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713175.1	s__JADJPQ01 sp016713175	77.0054	399	2348	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JADJPQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:59:00,324] [INFO] GTDB search result was written to OceanDNA-b23093/result_gtdb.tsv
[2023-03-18 20:59:00,324] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:59:00,325] [INFO] DFAST_QC result json was written to OceanDNA-b23093/dqc_result.json
[2023-03-18 20:59:00,325] [INFO] DFAST_QC completed!
[2023-03-18 20:59:00,325] [INFO] Total running time: 0h3m11s