[2023-06-16 23:00:03,764] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:00:03,771] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:00:03,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg41995ddf-4e83-4e22-80a5-3c6fc5aef384/dqc_reference
[2023-06-16 23:00:05,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:00:05,011] [INFO] Task started: Prodigal
[2023-06-16 23:00:05,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg2151d37f-62e4-449b-b40c-a6c3cb55d51a/GCA_009698525.1_ASM969852v1_genomic.fna.gz | prodigal -d GCA_009698525.1_ASM969852v1_genomic.fna/cds.fna -a GCA_009698525.1_ASM969852v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:00:16,078] [INFO] Task succeeded: Prodigal
[2023-06-16 23:00:16,079] [INFO] Task started: HMMsearch
[2023-06-16 23:00:16,079] [INFO] Running command: hmmsearch --tblout GCA_009698525.1_ASM969852v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41995ddf-4e83-4e22-80a5-3c6fc5aef384/dqc_reference/reference_markers.hmm GCA_009698525.1_ASM969852v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:00:16,271] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:00:16,272] [INFO] Found 6/6 markers.
[2023-06-16 23:00:16,304] [INFO] Query marker FASTA was written to GCA_009698525.1_ASM969852v1_genomic.fna/markers.fasta
[2023-06-16 23:00:16,304] [INFO] Task started: Blastn
[2023-06-16 23:00:16,304] [INFO] Running command: blastn -query GCA_009698525.1_ASM969852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41995ddf-4e83-4e22-80a5-3c6fc5aef384/dqc_reference/reference_markers.fasta -out GCA_009698525.1_ASM969852v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:00:17,052] [INFO] Task succeeded: Blastn
[2023-06-16 23:00:17,057] [INFO] Selected 18 target genomes.
[2023-06-16 23:00:17,057] [INFO] Target genome list was writen to GCA_009698525.1_ASM969852v1_genomic.fna/target_genomes.txt
[2023-06-16 23:00:17,065] [INFO] Task started: fastANI
[2023-06-16 23:00:17,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg2151d37f-62e4-449b-b40c-a6c3cb55d51a/GCA_009698525.1_ASM969852v1_genomic.fna.gz --refList GCA_009698525.1_ASM969852v1_genomic.fna/target_genomes.txt --output GCA_009698525.1_ASM969852v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:00:30,875] [INFO] Task succeeded: fastANI
[2023-06-16 23:00:30,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41995ddf-4e83-4e22-80a5-3c6fc5aef384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:00:30,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41995ddf-4e83-4e22-80a5-3c6fc5aef384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:00:30,888] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:00:30,888] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 23:00:30,888] [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
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.3232	244	1090	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.144	235	1090	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.9273	238	1090	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.7379	164	1090	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.546	125	1090	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.1945	141	1090	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.0208	102	1090	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	75.3773	60	1090	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.3773	60	1090	95	below_threshold
Actinoplanes missouriensis	strain=431	GCA_000284295.1	1866	1866	type	True	75.3388	82	1090	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	75.3154	96	1090	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	75.2126	91	1090	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 23:00:30,895] [INFO] DFAST Taxonomy check result was written to GCA_009698525.1_ASM969852v1_genomic.fna/tc_result.tsv
[2023-06-16 23:00:30,896] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:00:30,896] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:00:30,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41995ddf-4e83-4e22-80a5-3c6fc5aef384/dqc_reference/checkm_data
[2023-06-16 23:00:30,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:00:30,935] [INFO] Task started: CheckM
[2023-06-16 23:00:30,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009698525.1_ASM969852v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009698525.1_ASM969852v1_genomic.fna/checkm_input GCA_009698525.1_ASM969852v1_genomic.fna/checkm_result
[2023-06-16 23:01:11,705] [INFO] Task succeeded: CheckM
[2023-06-16 23:01:11,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 23:01:11,727] [INFO] ===== Completeness check finished =====
[2023-06-16 23:01:11,727] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:01:11,727] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009698525.1_ASM969852v1_genomic.fna/markers.fasta)
[2023-06-16 23:01:11,728] [INFO] Task started: Blastn
[2023-06-16 23:01:11,728] [INFO] Running command: blastn -query GCA_009698525.1_ASM969852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41995ddf-4e83-4e22-80a5-3c6fc5aef384/dqc_reference/reference_markers_gtdb.fasta -out GCA_009698525.1_ASM969852v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:01:12,866] [INFO] Task succeeded: Blastn
[2023-06-16 23:01:12,871] [INFO] Selected 10 target genomes.
[2023-06-16 23:01:12,871] [INFO] Target genome list was writen to GCA_009698525.1_ASM969852v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:01:12,874] [INFO] Task started: fastANI
[2023-06-16 23:01:12,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg2151d37f-62e4-449b-b40c-a6c3cb55d51a/GCA_009698525.1_ASM969852v1_genomic.fna.gz --refList GCA_009698525.1_ASM969852v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009698525.1_ASM969852v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:01:21,101] [INFO] Task succeeded: fastANI
[2023-06-16 23:01:21,110] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 23:01:21,111] [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_009702045.1	s__UBA668 sp009702045	99.9509	1069	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.96	99.94	0.98	0.97	6	conclusive
GCA_903919215.1	s__UBA668 sp903919215	93.1676	777	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016722025.1	s__UBA668 sp002299395	79.8407	533	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.06	98.90	0.95	0.90	7	-
GCA_016213625.1	s__UBA668 sp016213625	79.5075	484	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919455.1	s__UBA668 sp903919455	79.0645	405	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.17	98.79	0.93	0.92	4	-
GCA_005778215.1	s__UBA668 sp005778215	78.8554	410	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.54	99.53	0.90	0.89	3	-
GCA_003154135.1	s__UBA668 sp003154135	78.6528	402	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871355.1	s__Casp-actino8 sp016871355	77.0196	141	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882725.1	s__Casp-actino8 sp018882725	76.7772	123	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	76.7379	164	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 23:01:21,112] [INFO] GTDB search result was written to GCA_009698525.1_ASM969852v1_genomic.fna/result_gtdb.tsv
[2023-06-16 23:01:21,113] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:01:21,116] [INFO] DFAST_QC result json was written to GCA_009698525.1_ASM969852v1_genomic.fna/dqc_result.json
[2023-06-16 23:01:21,116] [INFO] DFAST_QC completed!
[2023-06-16 23:01:21,117] [INFO] Total running time: 0h1m17s