[2023-06-08 05:14:40,092] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:14:40,094] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:14:40,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg162e5bec-8322-4cba-b189-3d1e5e8a2c20/dqc_reference
[2023-06-08 05:14:42,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:14:42,413] [INFO] Task started: Prodigal
[2023-06-08 05:14:42,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d340549-bc1e-416d-b39b-20b8404c7a4d/GCA_945878355.1_MiH-16apr19-37_genomic.fna.gz | prodigal -d GCA_945878355.1_MiH-16apr19-37_genomic.fna/cds.fna -a GCA_945878355.1_MiH-16apr19-37_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:15:00,847] [INFO] Task succeeded: Prodigal
[2023-06-08 05:15:00,848] [INFO] Task started: HMMsearch
[2023-06-08 05:15:00,848] [INFO] Running command: hmmsearch --tblout GCA_945878355.1_MiH-16apr19-37_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg162e5bec-8322-4cba-b189-3d1e5e8a2c20/dqc_reference/reference_markers.hmm GCA_945878355.1_MiH-16apr19-37_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:15:01,166] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:15:01,167] [INFO] Found 6/6 markers.
[2023-06-08 05:15:01,216] [INFO] Query marker FASTA was written to GCA_945878355.1_MiH-16apr19-37_genomic.fna/markers.fasta
[2023-06-08 05:15:01,217] [INFO] Task started: Blastn
[2023-06-08 05:15:01,217] [INFO] Running command: blastn -query GCA_945878355.1_MiH-16apr19-37_genomic.fna/markers.fasta -db /var/lib/cwl/stg162e5bec-8322-4cba-b189-3d1e5e8a2c20/dqc_reference/reference_markers.fasta -out GCA_945878355.1_MiH-16apr19-37_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:15:02,164] [INFO] Task succeeded: Blastn
[2023-06-08 05:15:02,169] [INFO] Selected 23 target genomes.
[2023-06-08 05:15:02,169] [INFO] Target genome list was writen to GCA_945878355.1_MiH-16apr19-37_genomic.fna/target_genomes.txt
[2023-06-08 05:15:02,175] [INFO] Task started: fastANI
[2023-06-08 05:15:02,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d340549-bc1e-416d-b39b-20b8404c7a4d/GCA_945878355.1_MiH-16apr19-37_genomic.fna.gz --refList GCA_945878355.1_MiH-16apr19-37_genomic.fna/target_genomes.txt --output GCA_945878355.1_MiH-16apr19-37_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:15:21,820] [INFO] Task succeeded: fastANI
[2023-06-08 05:15:21,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg162e5bec-8322-4cba-b189-3d1e5e8a2c20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:15:21,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg162e5bec-8322-4cba-b189-3d1e5e8a2c20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:15:21,841] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:15:21,841] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:15:21,842] [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
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	79.401	524	1730	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	79.3978	527	1730	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	79.1225	573	1730	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	79.0744	566	1730	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	78.9793	488	1730	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	78.973	435	1730	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.9622	505	1730	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.7904	479	1730	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.7851	486	1730	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	78.7095	481	1730	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	78.6187	494	1730	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.5714	471	1730	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	78.4559	541	1730	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	78.4485	555	1730	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.3241	531	1730	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.2038	464	1730	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.0149	458	1730	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.9244	419	1730	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	77.3814	315	1730	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.6116	263	1730	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	75.9681	167	1730	95	below_threshold
Duganella flavida	strain=FT135W	GCA_009857445.1	2692175	2692175	type	True	75.8245	176	1730	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:15:21,844] [INFO] DFAST Taxonomy check result was written to GCA_945878355.1_MiH-16apr19-37_genomic.fna/tc_result.tsv
[2023-06-08 05:15:21,844] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:15:21,844] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:15:21,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg162e5bec-8322-4cba-b189-3d1e5e8a2c20/dqc_reference/checkm_data
[2023-06-08 05:15:21,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:15:21,905] [INFO] Task started: CheckM
[2023-06-08 05:15:21,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945878355.1_MiH-16apr19-37_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945878355.1_MiH-16apr19-37_genomic.fna/checkm_input GCA_945878355.1_MiH-16apr19-37_genomic.fna/checkm_result
[2023-06-08 05:16:24,180] [INFO] Task succeeded: CheckM
[2023-06-08 05:16:24,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:16:24,206] [INFO] ===== Completeness check finished =====
[2023-06-08 05:16:24,207] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:16:24,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945878355.1_MiH-16apr19-37_genomic.fna/markers.fasta)
[2023-06-08 05:16:24,208] [INFO] Task started: Blastn
[2023-06-08 05:16:24,208] [INFO] Running command: blastn -query GCA_945878355.1_MiH-16apr19-37_genomic.fna/markers.fasta -db /var/lib/cwl/stg162e5bec-8322-4cba-b189-3d1e5e8a2c20/dqc_reference/reference_markers_gtdb.fasta -out GCA_945878355.1_MiH-16apr19-37_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:16:26,165] [INFO] Task succeeded: Blastn
[2023-06-08 05:16:26,170] [INFO] Selected 17 target genomes.
[2023-06-08 05:16:26,170] [INFO] Target genome list was writen to GCA_945878355.1_MiH-16apr19-37_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:16:26,185] [INFO] Task started: fastANI
[2023-06-08 05:16:26,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d340549-bc1e-416d-b39b-20b8404c7a4d/GCA_945878355.1_MiH-16apr19-37_genomic.fna.gz --refList GCA_945878355.1_MiH-16apr19-37_genomic.fna/target_genomes_gtdb.txt --output GCA_945878355.1_MiH-16apr19-37_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:16:43,948] [INFO] Task succeeded: fastANI
[2023-06-08 05:16:43,966] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 05:16:43,967] [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_010030205.1	s__Aquabacterium_A sp010030205	93.2441	1090	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770815.1	s__Aquabacterium_A sp001770815	81.7072	771	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790515.1	s__Aquabacterium_A sp016790515	81.5141	700	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005403045.1	s__Aquabacterium_A pictum	80.8589	840	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999135.1	s__Aquabacterium_A sp017999135	80.2053	511	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	80.1812	755	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	80.0687	766	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266755.1	s__Aquabacterium_A terrae	79.5794	707	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721465.1	s__Aquabacterium_A sp016721465	79.5012	672	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	98.92	98.92	0.93	0.93	2	-
GCF_016583785.1	s__Rubrivivax gelatinosus_B	79.1169	554	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.02	99.02	0.92	0.92	2	-
GCF_004340905.1	s__Rubrivivax gelatinosus	79.0877	577	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003201595.1	s__Sphaerotilus hippei	79.0474	480	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799605.1	s__Rhizobacter sp000799605	78.7625	562	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817345.1	s__Methylibium sp013817345	78.4496	344	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525985.1	s__Rubrivivax sp011525985	78.1581	257	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464055.1	s__Rubrivivax sp001464055	77.9959	461	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	77.7924	390	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 05:16:43,969] [INFO] GTDB search result was written to GCA_945878355.1_MiH-16apr19-37_genomic.fna/result_gtdb.tsv
[2023-06-08 05:16:43,970] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:16:43,974] [INFO] DFAST_QC result json was written to GCA_945878355.1_MiH-16apr19-37_genomic.fna/dqc_result.json
[2023-06-08 05:16:43,975] [INFO] DFAST_QC completed!
[2023-06-08 05:16:43,975] [INFO] Total running time: 0h2m4s