[2024-01-24 13:19:00,798] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:00,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:00,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg52e2cd9c-08f7-4365-88de-ebed6e151c97/dqc_reference
[2024-01-24 13:19:02,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,103] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b045487-a946-47dd-b791-858b159fbdbe/GCF_007829565.1_ASM782956v1_genomic.fna.gz | prodigal -d GCF_007829565.1_ASM782956v1_genomic.fna/cds.fna -a GCF_007829565.1_ASM782956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:18,567] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:18,568] [INFO] Task started: HMMsearch
[2024-01-24 13:19:18,568] [INFO] Running command: hmmsearch --tblout GCF_007829565.1_ASM782956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52e2cd9c-08f7-4365-88de-ebed6e151c97/dqc_reference/reference_markers.hmm GCF_007829565.1_ASM782956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:18,925] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:18,926] [INFO] Found 6/6 markers.
[2024-01-24 13:19:18,970] [INFO] Query marker FASTA was written to GCF_007829565.1_ASM782956v1_genomic.fna/markers.fasta
[2024-01-24 13:19:18,971] [INFO] Task started: Blastn
[2024-01-24 13:19:18,971] [INFO] Running command: blastn -query GCF_007829565.1_ASM782956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e2cd9c-08f7-4365-88de-ebed6e151c97/dqc_reference/reference_markers.fasta -out GCF_007829565.1_ASM782956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:20,456] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:20,459] [INFO] Selected 17 target genomes.
[2024-01-24 13:19:20,460] [INFO] Target genome list was writen to GCF_007829565.1_ASM782956v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:20,469] [INFO] Task started: fastANI
[2024-01-24 13:19:20,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b045487-a946-47dd-b791-858b159fbdbe/GCF_007829565.1_ASM782956v1_genomic.fna.gz --refList GCF_007829565.1_ASM782956v1_genomic.fna/target_genomes.txt --output GCF_007829565.1_ASM782956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:44,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:44,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52e2cd9c-08f7-4365-88de-ebed6e151c97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:44,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52e2cd9c-08f7-4365-88de-ebed6e151c97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:44,148] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:44,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:44,149] [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
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	100.0	1759	1759	95	conclusive
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	99.9794	1702	1759	95	conclusive
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	84.4199	1281	1759	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	84.1577	1303	1759	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.5055	972	1759	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	80.4002	947	1759	95	below_threshold
Saccharomonospora iraqiensis	strain=IQ-H1	GCA_000430445.1	52698	52698	type	True	79.6969	591	1759	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.646	798	1759	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	79.6005	734	1759	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	79.5063	746	1759	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	79.4969	750	1759	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.876	809	1759	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	78.6658	766	1759	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	78.6607	776	1759	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	77.6447	594	1759	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	77.1447	511	1759	95	below_threshold
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	77.0363	499	1759	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:44,150] [INFO] DFAST Taxonomy check result was written to GCF_007829565.1_ASM782956v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:44,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:44,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:44,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52e2cd9c-08f7-4365-88de-ebed6e151c97/dqc_reference/checkm_data
[2024-01-24 13:19:44,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:44,202] [INFO] Task started: CheckM
[2024-01-24 13:19:44,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007829565.1_ASM782956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007829565.1_ASM782956v1_genomic.fna/checkm_input GCF_007829565.1_ASM782956v1_genomic.fna/checkm_result
[2024-01-24 13:21:17,482] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:17,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:17,504] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:17,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:17,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007829565.1_ASM782956v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:17,505] [INFO] Task started: Blastn
[2024-01-24 13:21:17,505] [INFO] Running command: blastn -query GCF_007829565.1_ASM782956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e2cd9c-08f7-4365-88de-ebed6e151c97/dqc_reference/reference_markers_gtdb.fasta -out GCF_007829565.1_ASM782956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:19,590] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:19,594] [INFO] Selected 17 target genomes.
[2024-01-24 13:21:19,594] [INFO] Target genome list was writen to GCF_007829565.1_ASM782956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:19,612] [INFO] Task started: fastANI
[2024-01-24 13:21:19,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b045487-a946-47dd-b791-858b159fbdbe/GCF_007829565.1_ASM782956v1_genomic.fna.gz --refList GCF_007829565.1_ASM782956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007829565.1_ASM782956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:42,060] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:42,077] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:42,078] [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
GCF_000719975.1	s__Saccharomonospora rugosa	99.9794	1702	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	conclusive
GCF_001942305.1	s__Saccharomonospora sp001942305	86.1866	1254	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191605.1	s__Saccharomonospora isguenensis	84.1499	1304	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195435.1	s__Saccharomonospora sediminis	83.9744	1277	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.5741	1012	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595675.1	s__Saccharomonospora sp016595675	80.4683	978	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	80.3583	984	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_000430445.1	s__Saccharomonospora iraqiensis	79.6573	596	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	79.4505	757	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002262875.1	s__Amycolatopsis antarctica	79.121	701	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018885265.1	s__Amycolatopsis_D sp018885265	78.9713	718	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	78.6633	789	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995215.1	s__Amycolatopsis azurea	78.6547	777	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000826545.1	s__Kibdelosporangium sp000826545	77.5487	580	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	77.1056	519	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933465.1	s__Actinomycetospora sp012933465	76.895	493	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289575.1	s__Dietzia natronolimnaea_A	76.6196	205	1759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	96.66	96.66	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:42,080] [INFO] GTDB search result was written to GCF_007829565.1_ASM782956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:42,081] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:42,084] [INFO] DFAST_QC result json was written to GCF_007829565.1_ASM782956v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:42,085] [INFO] DFAST_QC completed!
[2024-01-24 13:21:42,085] [INFO] Total running time: 0h2m41s