[2024-01-24 12:44:53,933] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:53,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:53,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a638cfc-20b2-4ed8-b94b-a898f34b6f5f/dqc_reference
[2024-01-24 12:44:55,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:55,230] [INFO] Task started: Prodigal
[2024-01-24 12:44:55,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg462c21bb-e490-4b0b-9dde-af8c0284d63a/GCF_016595675.1_ASM1659567v1_genomic.fna.gz | prodigal -d GCF_016595675.1_ASM1659567v1_genomic.fna/cds.fna -a GCF_016595675.1_ASM1659567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:20,078] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:20,078] [INFO] Task started: HMMsearch
[2024-01-24 12:45:20,079] [INFO] Running command: hmmsearch --tblout GCF_016595675.1_ASM1659567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a638cfc-20b2-4ed8-b94b-a898f34b6f5f/dqc_reference/reference_markers.hmm GCF_016595675.1_ASM1659567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:20,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:20,466] [INFO] Found 6/6 markers.
[2024-01-24 12:45:20,528] [INFO] Query marker FASTA was written to GCF_016595675.1_ASM1659567v1_genomic.fna/markers.fasta
[2024-01-24 12:45:20,528] [INFO] Task started: Blastn
[2024-01-24 12:45:20,528] [INFO] Running command: blastn -query GCF_016595675.1_ASM1659567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a638cfc-20b2-4ed8-b94b-a898f34b6f5f/dqc_reference/reference_markers.fasta -out GCF_016595675.1_ASM1659567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:21,889] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:21,893] [INFO] Selected 18 target genomes.
[2024-01-24 12:45:21,893] [INFO] Target genome list was writen to GCF_016595675.1_ASM1659567v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:21,907] [INFO] Task started: fastANI
[2024-01-24 12:45:21,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg462c21bb-e490-4b0b-9dde-af8c0284d63a/GCF_016595675.1_ASM1659567v1_genomic.fna.gz --refList GCF_016595675.1_ASM1659567v1_genomic.fna/target_genomes.txt --output GCF_016595675.1_ASM1659567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:47,956] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:47,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a638cfc-20b2-4ed8-b94b-a898f34b6f5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:47,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a638cfc-20b2-4ed8-b94b-a898f34b6f5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:47,976] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:47,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:47,976] [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 cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	100.0	2378	2380	95	conclusive
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	82.6697	1328	2380	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	82.6136	1319	2380	95	below_threshold
Prauserella marina	strain=DSM 45268	GCA_002240355.1	530584	530584	type	True	80.8554	1190	2380	95	below_threshold
Prauserella marina	strain=DSM 45268	GCA_003182115.1	530584	530584	type	True	80.8265	1172	2380	95	below_threshold
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	80.5386	980	2380	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	80.492	985	2380	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	80.3177	1007	2380	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.2574	1075	2380	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	80.255	1017	2380	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	80.2369	959	2380	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	80.0756	938	2380	95	below_threshold
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	80.0518	1008	2380	95	below_threshold
Saccharomonospora iraqiensis subsp. paurometabolica	strain=YIM 90007	GCA_000231035.3	208085	52698	type	True	79.9371	788	2380	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	79.9167	1054	2380	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	79.8908	1070	2380	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.4005	1030	2380	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	79.2206	1145	2380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:47,978] [INFO] DFAST Taxonomy check result was written to GCF_016595675.1_ASM1659567v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:47,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:47,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:47,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a638cfc-20b2-4ed8-b94b-a898f34b6f5f/dqc_reference/checkm_data
[2024-01-24 12:45:47,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:48,045] [INFO] Task started: CheckM
[2024-01-24 12:45:48,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595675.1_ASM1659567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595675.1_ASM1659567v1_genomic.fna/checkm_input GCF_016595675.1_ASM1659567v1_genomic.fna/checkm_result
[2024-01-24 12:47:06,655] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:06,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:06,682] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:06,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:06,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595675.1_ASM1659567v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:06,683] [INFO] Task started: Blastn
[2024-01-24 12:47:06,683] [INFO] Running command: blastn -query GCF_016595675.1_ASM1659567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a638cfc-20b2-4ed8-b94b-a898f34b6f5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595675.1_ASM1659567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:08,712] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:08,716] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:08,717] [INFO] Target genome list was writen to GCF_016595675.1_ASM1659567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:08,728] [INFO] Task started: fastANI
[2024-01-24 12:47:08,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg462c21bb-e490-4b0b-9dde-af8c0284d63a/GCF_016595675.1_ASM1659567v1_genomic.fna.gz --refList GCF_016595675.1_ASM1659567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016595675.1_ASM1659567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:30,049] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:30,060] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:30,061] [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_016595675.1	s__Saccharomonospora sp016595675	100.0	2378	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003202235.1	s__Saccharomonospora sp003202235	86.2218	1664	2380	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	86.0073	1591	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_003202285.1	s__Saccharomonospora muralis	82.5946	1323	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	81.6078	1192	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464705.1	s__Saccharomonospora sp016464705	81.5054	1168	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002240355.1	s__Saccharomonospora marina_A	80.8694	1187	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000719975.1	s__Saccharomonospora rugosa	80.5344	980	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	-
GCF_900115565.1	s__Yuhushiella arida	80.3188	1008	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003385215.1	s__Amycolatopsis thermalba	80.2585	1074	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.72	99.30	0.96	0.93	4	-
GCF_014653945.1	s__Amycolatopsis deserti	80.1085	1109	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713745.1	s__Amycolatopsis acidiphila	80.0654	1006	2380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:30,062] [INFO] GTDB search result was written to GCF_016595675.1_ASM1659567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:30,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:30,067] [INFO] DFAST_QC result json was written to GCF_016595675.1_ASM1659567v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:30,067] [INFO] DFAST_QC completed!
[2024-01-24 12:47:30,067] [INFO] Total running time: 0h2m36s