[2024-01-24 12:46:57,491] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:57,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:57,493] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f74696b-ddc0-4cea-8aac-f4ea75fb7a2e/dqc_reference
[2024-01-24 12:46:58,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:58,942] [INFO] Task started: Prodigal
[2024-01-24 12:46:58,943] [INFO] Running command: gunzip -c /var/lib/cwl/stgf45cfdbf-9e38-4c9b-a38a-cbb25e84f2db/GCF_000430445.1_ASM43044v1_genomic.fna.gz | prodigal -d GCF_000430445.1_ASM43044v1_genomic.fna/cds.fna -a GCF_000430445.1_ASM43044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:09,907] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:09,908] [INFO] Task started: HMMsearch
[2024-01-24 12:47:09,908] [INFO] Running command: hmmsearch --tblout GCF_000430445.1_ASM43044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f74696b-ddc0-4cea-8aac-f4ea75fb7a2e/dqc_reference/reference_markers.hmm GCF_000430445.1_ASM43044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:10,189] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:10,190] [INFO] Found 6/6 markers.
[2024-01-24 12:47:10,222] [INFO] Query marker FASTA was written to GCF_000430445.1_ASM43044v1_genomic.fna/markers.fasta
[2024-01-24 12:47:10,222] [INFO] Task started: Blastn
[2024-01-24 12:47:10,223] [INFO] Running command: blastn -query GCF_000430445.1_ASM43044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f74696b-ddc0-4cea-8aac-f4ea75fb7a2e/dqc_reference/reference_markers.fasta -out GCF_000430445.1_ASM43044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:11,472] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:11,475] [INFO] Selected 17 target genomes.
[2024-01-24 12:47:11,475] [INFO] Target genome list was writen to GCF_000430445.1_ASM43044v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:11,481] [INFO] Task started: fastANI
[2024-01-24 12:47:11,481] [INFO] Running command: fastANI --query /var/lib/cwl/stgf45cfdbf-9e38-4c9b-a38a-cbb25e84f2db/GCF_000430445.1_ASM43044v1_genomic.fna.gz --refList GCF_000430445.1_ASM43044v1_genomic.fna/target_genomes.txt --output GCF_000430445.1_ASM43044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:32,264] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:32,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f74696b-ddc0-4cea-8aac-f4ea75fb7a2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:32,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f74696b-ddc0-4cea-8aac-f4ea75fb7a2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:32,279] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:32,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:32,279] [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
Saccharomonospora iraqiensis	strain=IQ-H1	GCA_000430445.1	52698	52698	type	True	99.9999	1219	1223	95	conclusive
Saccharomonospora iraqiensis subsp. paurometabolica	strain=YIM 90007	GCA_000231035.3	208085	52698	type	True	96.0038	1061	1223	95	conclusive
Saccharomonospora halophila	strain=8	GCA_000383775.1	129922	129922	type	True	93.3901	907	1223	95	below_threshold
Saccharomonospora saliphila	strain=YIM 90502	GCA_000383795.1	369829	369829	type	True	83.4578	773	1223	95	below_threshold
Saccharomonospora piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	80.6439	697	1223	95	below_threshold
Saccharomonospora azurea	strain=NA-128	GCA_000231055.3	40988	40988	type	True	80.6344	698	1223	95	below_threshold
Saccharomonospora cyanea	strain=NA-134	GCA_000244975.1	40989	40989	type	True	80.6278	709	1223	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	80.0805	671	1223	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.0666	694	1223	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	80.0335	688	1223	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	79.6365	635	1223	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.5427	659	1223	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.2731	691	1223	95	below_threshold
Amycolatopsis alkalitolerans	strain=SYSUP0005	GCA_006152065.1	2547244	2547244	type	True	78.8639	569	1223	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.6131	657	1223	95	below_threshold
Haloechinothrix aidingensis	strain=YIM 98757	GCA_013450155.1	2752311	2752311	type	True	78.485	434	1223	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.1183	510	1223	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:32,281] [INFO] DFAST Taxonomy check result was written to GCF_000430445.1_ASM43044v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:32,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:32,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:32,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f74696b-ddc0-4cea-8aac-f4ea75fb7a2e/dqc_reference/checkm_data
[2024-01-24 12:47:32,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:32,330] [INFO] Task started: CheckM
[2024-01-24 12:47:32,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430445.1_ASM43044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430445.1_ASM43044v1_genomic.fna/checkm_input GCF_000430445.1_ASM43044v1_genomic.fna/checkm_result
[2024-01-24 12:48:03,346] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:03,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:03,369] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:03,369] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:03,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430445.1_ASM43044v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:03,370] [INFO] Task started: Blastn
[2024-01-24 12:48:03,370] [INFO] Running command: blastn -query GCF_000430445.1_ASM43044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f74696b-ddc0-4cea-8aac-f4ea75fb7a2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430445.1_ASM43044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:05,265] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:05,268] [INFO] Selected 12 target genomes.
[2024-01-24 12:48:05,268] [INFO] Target genome list was writen to GCF_000430445.1_ASM43044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:05,278] [INFO] Task started: fastANI
[2024-01-24 12:48:05,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgf45cfdbf-9e38-4c9b-a38a-cbb25e84f2db/GCF_000430445.1_ASM43044v1_genomic.fna.gz --refList GCF_000430445.1_ASM43044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430445.1_ASM43044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:19,162] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:19,178] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:48:19,179] [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_000430445.1	s__Saccharomonospora iraqiensis	99.9999	1219	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000231035.2	s__Saccharomonospora paurometabolica	96.0056	1060	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000383775.1	s__Saccharomonospora halophila	93.3955	906	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383795.1	s__Saccharomonospora saliphila	83.4693	772	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	80.67	718	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005862235.1	s__Saccharomonospora piscinae	80.6369	697	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	98.79	98.27	0.95	0.94	3	-
GCF_016464705.1	s__Saccharomonospora sp016464705	80.3056	703	1223	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	80.2259	720	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_900115565.1	s__Yuhushiella arida	80.0433	677	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017875555.1	s__Amycolatopsis magusensis	79.2136	675	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006152065.1	s__Amycolatopsis alkalitolerans	78.8652	570	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013450155.1	s__Haloechinothrix aidingensis	78.4438	440	1223	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Haloechinothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:19,180] [INFO] GTDB search result was written to GCF_000430445.1_ASM43044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:19,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:19,187] [INFO] DFAST_QC result json was written to GCF_000430445.1_ASM43044v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:19,188] [INFO] DFAST_QC completed!
[2024-01-24 12:48:19,188] [INFO] Total running time: 0h1m22s