[2023-03-19 00:19:08,846] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:19:08,846] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:19:08,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg183aef11-cc27-4eac-8edd-27c3f9d307d6/dqc_reference
[2023-03-19 00:19:10,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:19:10,375] [INFO] Task started: Prodigal
[2023-03-19 00:19:10,375] [INFO] Running command: cat /var/lib/cwl/stg25f30bca-6295-4e9d-b5a2-d372deb3e568/OceanDNA-b46675.fa | prodigal -d OceanDNA-b46675/cds.fna -a OceanDNA-b46675/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:19:32,987] [INFO] Task succeeded: Prodigal
[2023-03-19 00:19:32,988] [INFO] Task started: HMMsearch
[2023-03-19 00:19:32,988] [INFO] Running command: hmmsearch --tblout OceanDNA-b46675/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg183aef11-cc27-4eac-8edd-27c3f9d307d6/dqc_reference/reference_markers.hmm OceanDNA-b46675/protein.faa > /dev/null
[2023-03-19 00:19:33,162] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:19:33,163] [INFO] Found 6/6 markers.
[2023-03-19 00:19:33,179] [INFO] Query marker FASTA was written to OceanDNA-b46675/markers.fasta
[2023-03-19 00:19:33,181] [INFO] Task started: Blastn
[2023-03-19 00:19:33,181] [INFO] Running command: blastn -query OceanDNA-b46675/markers.fasta -db /var/lib/cwl/stg183aef11-cc27-4eac-8edd-27c3f9d307d6/dqc_reference/reference_markers.fasta -out OceanDNA-b46675/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:19:33,711] [INFO] Task succeeded: Blastn
[2023-03-19 00:19:33,712] [INFO] Selected 23 target genomes.
[2023-03-19 00:19:33,712] [INFO] Target genome list was writen to OceanDNA-b46675/target_genomes.txt
[2023-03-19 00:19:33,728] [INFO] Task started: fastANI
[2023-03-19 00:19:33,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg25f30bca-6295-4e9d-b5a2-d372deb3e568/OceanDNA-b46675.fa --refList OceanDNA-b46675/target_genomes.txt --output OceanDNA-b46675/fastani_result.tsv --threads 1
[2023-03-19 00:19:49,828] [INFO] Task succeeded: fastANI
[2023-03-19 00:19:49,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg183aef11-cc27-4eac-8edd-27c3f9d307d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:19:49,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg183aef11-cc27-4eac-8edd-27c3f9d307d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:19:49,836] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:19:49,836] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:19:49,836] [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
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.5847	100	832	95	below_threshold
Roseibacillus ishigakijimensis	strain=KCTC 12986	GCA_016595415.1	454146	454146	type	True	76.3866	73	832	95	below_threshold
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	76.3579	62	832	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.2659	73	832	95	below_threshold
Roseibacillus persicicus	strain=KCTC 12988	GCA_014651675.1	454148	454148	type	True	76.0363	61	832	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	75.8656	61	832	95	below_threshold
Phragmitibacter flavus	strain=MG-N-17	GCA_005780165.1	2576071	2576071	type	True	75.7978	55	832	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	75.7755	62	832	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:19:49,836] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46675/tc_result.tsv
[2023-03-19 00:19:49,837] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:19:49,837] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:19:49,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg183aef11-cc27-4eac-8edd-27c3f9d307d6/dqc_reference/checkm_data
[2023-03-19 00:19:49,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:19:49,842] [INFO] Task started: CheckM
[2023-03-19 00:19:49,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46675/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46675/checkm_input OceanDNA-b46675/checkm_result
[2023-03-19 00:20:48,338] [INFO] Task succeeded: CheckM
[2023-03-19 00:20:48,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:20:48,341] [INFO] ===== Completeness check finished =====
[2023-03-19 00:20:48,341] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:20:48,342] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46675/markers.fasta)
[2023-03-19 00:20:48,343] [INFO] Task started: Blastn
[2023-03-19 00:20:48,343] [INFO] Running command: blastn -query OceanDNA-b46675/markers.fasta -db /var/lib/cwl/stg183aef11-cc27-4eac-8edd-27c3f9d307d6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46675/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:20:49,106] [INFO] Task succeeded: Blastn
[2023-03-19 00:20:49,107] [INFO] Selected 21 target genomes.
[2023-03-19 00:20:49,107] [INFO] Target genome list was writen to OceanDNA-b46675/target_genomes_gtdb.txt
[2023-03-19 00:20:49,154] [INFO] Task started: fastANI
[2023-03-19 00:20:49,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg25f30bca-6295-4e9d-b5a2-d372deb3e568/OceanDNA-b46675.fa --refList OceanDNA-b46675/target_genomes_gtdb.txt --output OceanDNA-b46675/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:21:02,372] [INFO] Task succeeded: fastANI
[2023-03-19 00:21:02,380] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:21:02,380] [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_013001695.1	s__Roseibacillus_B sp013001695	76.8028	169	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304315.1	s__Haloferula sp002304315	76.6788	78	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595525.1	s__Haloferula rosea	76.5847	100	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595415.1	s__Roseibacillus ishigakijimensis	76.3866	73	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739615.1	s__Haloferula sp000739615	76.3352	65	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016811075.1	s__UBA985 sp016811075	76.2948	53	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
GCF_018137965.1	s__Luteolibacter sp018137965	76.2659	73	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501065.1	s__Roseibacillus_B sp002501065	76.1812	77	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.61	99.55	0.90	0.89	3	-
GCA_002721695.1	s__Roseibacillus_B sp002721695	75.9361	68	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003820635.1	s__Luteolibacter sp003820635	75.9282	58	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	75.9091	59	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483645.1	s__Roseibacillus_B sp003483645	75.9075	56	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595465.1	s__Luteolibacter yonseiensis	75.7922	61	832	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:21:02,380] [INFO] GTDB search result was written to OceanDNA-b46675/result_gtdb.tsv
[2023-03-19 00:21:02,380] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:21:02,382] [INFO] DFAST_QC result json was written to OceanDNA-b46675/dqc_result.json
[2023-03-19 00:21:02,382] [INFO] DFAST_QC completed!
[2023-03-19 00:21:02,382] [INFO] Total running time: 0h1m54s