[2023-06-30 09:06:25,147] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:06:25,149] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:06:25,149] [INFO] DQC Reference Directory: /var/lib/cwl/stga5827498-8c4e-4a5c-8dcc-0ddccd4226b1/dqc_reference
[2023-06-30 09:06:26,363] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:06:26,364] [INFO] Task started: Prodigal
[2023-06-30 09:06:26,364] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b511555-a17b-42f5-b969-a29813760917/GCA_019247495.1_ASM1924749v1_genomic.fna.gz | prodigal -d GCA_019247495.1_ASM1924749v1_genomic.fna/cds.fna -a GCA_019247495.1_ASM1924749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:06:40,433] [INFO] Task succeeded: Prodigal
[2023-06-30 09:06:40,434] [INFO] Task started: HMMsearch
[2023-06-30 09:06:40,434] [INFO] Running command: hmmsearch --tblout GCA_019247495.1_ASM1924749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5827498-8c4e-4a5c-8dcc-0ddccd4226b1/dqc_reference/reference_markers.hmm GCA_019247495.1_ASM1924749v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:06:40,729] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:06:40,730] [INFO] Found 6/6 markers.
[2023-06-30 09:06:40,775] [INFO] Query marker FASTA was written to GCA_019247495.1_ASM1924749v1_genomic.fna/markers.fasta
[2023-06-30 09:06:40,775] [INFO] Task started: Blastn
[2023-06-30 09:06:40,775] [INFO] Running command: blastn -query GCA_019247495.1_ASM1924749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5827498-8c4e-4a5c-8dcc-0ddccd4226b1/dqc_reference/reference_markers.fasta -out GCA_019247495.1_ASM1924749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:06:41,404] [INFO] Task succeeded: Blastn
[2023-06-30 09:06:41,409] [INFO] Selected 34 target genomes.
[2023-06-30 09:06:41,409] [INFO] Target genome list was writen to GCA_019247495.1_ASM1924749v1_genomic.fna/target_genomes.txt
[2023-06-30 09:06:41,413] [INFO] Task started: fastANI
[2023-06-30 09:06:41,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b511555-a17b-42f5-b969-a29813760917/GCA_019247495.1_ASM1924749v1_genomic.fna.gz --refList GCA_019247495.1_ASM1924749v1_genomic.fna/target_genomes.txt --output GCA_019247495.1_ASM1924749v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:07:01,798] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:01,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5827498-8c4e-4a5c-8dcc-0ddccd4226b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:07:01,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5827498-8c4e-4a5c-8dcc-0ddccd4226b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:07:01,818] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:07:01,818] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 09:07:01,818] [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
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	75.3518	57	1641	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	75.2386	79	1641	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	75.2109	55	1641	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.2094	55	1641	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	75.0072	51	1641	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	74.9912	57	1641	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	74.976	54	1641	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	74.9344	54	1641	95	below_threshold
Paraburkholderia acidipaludis	strain=NBRC 101816	GCA_000684975.1	660537	660537	type	True	74.9213	85	1641	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	74.9131	108	1641	95	below_threshold
Plantibacter flavus	strain=DSM 14012	GCA_003755125.1	150123	150123	type	True	74.9101	54	1641	95	below_threshold
Plantibacter flavus	strain=VKM Ac-2504	GCA_900177615.1	150123	150123	type	True	74.9101	54	1641	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	74.9085	72	1641	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	74.8919	99	1641	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	74.8732	96	1641	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	74.7945	115	1641	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	74.7307	68	1641	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	74.7108	59	1641	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	74.6651	68	1641	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 09:07:01,821] [INFO] DFAST Taxonomy check result was written to GCA_019247495.1_ASM1924749v1_genomic.fna/tc_result.tsv
[2023-06-30 09:07:01,822] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:07:01,822] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:07:01,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5827498-8c4e-4a5c-8dcc-0ddccd4226b1/dqc_reference/checkm_data
[2023-06-30 09:07:01,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:07:01,877] [INFO] Task started: CheckM
[2023-06-30 09:07:01,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019247495.1_ASM1924749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019247495.1_ASM1924749v1_genomic.fna/checkm_input GCA_019247495.1_ASM1924749v1_genomic.fna/checkm_result
[2023-06-30 09:07:45,468] [INFO] Task succeeded: CheckM
[2023-06-30 09:07:45,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:07:45,496] [INFO] ===== Completeness check finished =====
[2023-06-30 09:07:45,497] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:07:45,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019247495.1_ASM1924749v1_genomic.fna/markers.fasta)
[2023-06-30 09:07:45,497] [INFO] Task started: Blastn
[2023-06-30 09:07:45,498] [INFO] Running command: blastn -query GCA_019247495.1_ASM1924749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5827498-8c4e-4a5c-8dcc-0ddccd4226b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_019247495.1_ASM1924749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:07:46,421] [INFO] Task succeeded: Blastn
[2023-06-30 09:07:46,426] [INFO] Selected 10 target genomes.
[2023-06-30 09:07:46,426] [INFO] Target genome list was writen to GCA_019247495.1_ASM1924749v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:07:46,429] [INFO] Task started: fastANI
[2023-06-30 09:07:46,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b511555-a17b-42f5-b969-a29813760917/GCA_019247495.1_ASM1924749v1_genomic.fna.gz --refList GCA_019247495.1_ASM1924749v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019247495.1_ASM1924749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:07:57,536] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:57,544] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 09:07:57,545] [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_019247495.1	s__JADGNZ01 sp019247495	100.0	1631	1641	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	99.75	99.65	0.94	0.93	3	conclusive
GCA_017883235.1	s__JADGNZ01 sp017883235	81.6192	998	1641	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883205.1	s__JADGNZ01 sp017883205	80.7618	957	1641	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019244185.1	s__QHVT01 sp019244185	78.8915	647	1641	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_003223645.1	s__QHVT01 sp003223645	78.3659	619	1641	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242175.1	s__QHVT01 sp019242175	78.0789	479	1641	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223635.1	s__QHVS01 sp003223635	77.6495	369	1641	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650215.1	s__QHVT01 sp016650215	77.5766	301	1641	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220315.1	s__20CM-2-70-11 sp003220315	75.0321	79	1641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__20CM-2-70-11	95.0	99.38	99.31	0.92	0.87	7	-
--------------------------------------------------------------------------------
[2023-06-30 09:07:57,547] [INFO] GTDB search result was written to GCA_019247495.1_ASM1924749v1_genomic.fna/result_gtdb.tsv
[2023-06-30 09:07:57,547] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:07:57,551] [INFO] DFAST_QC result json was written to GCA_019247495.1_ASM1924749v1_genomic.fna/dqc_result.json
[2023-06-30 09:07:57,551] [INFO] DFAST_QC completed!
[2023-06-30 09:07:57,552] [INFO] Total running time: 0h1m32s