[2024-01-24 14:05:31,504] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,506] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f6d1e64-206a-4e4d-ae3c-74e060410c55/dqc_reference
[2024-01-24 14:05:32,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:32,674] [INFO] Task started: Prodigal
[2024-01-24 14:05:32,674] [INFO] Running command: gunzip -c /var/lib/cwl/stgeac910a0-7f24-419f-a58d-1a8275bbd8fb/GCF_007993965.1_ASM799396v1_genomic.fna.gz | prodigal -d GCF_007993965.1_ASM799396v1_genomic.fna/cds.fna -a GCF_007993965.1_ASM799396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:55,960] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:55,961] [INFO] Task started: HMMsearch
[2024-01-24 14:05:55,961] [INFO] Running command: hmmsearch --tblout GCF_007993965.1_ASM799396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f6d1e64-206a-4e4d-ae3c-74e060410c55/dqc_reference/reference_markers.hmm GCF_007993965.1_ASM799396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:56,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:56,337] [INFO] Found 6/6 markers.
[2024-01-24 14:05:56,397] [INFO] Query marker FASTA was written to GCF_007993965.1_ASM799396v1_genomic.fna/markers.fasta
[2024-01-24 14:05:56,397] [INFO] Task started: Blastn
[2024-01-24 14:05:56,397] [INFO] Running command: blastn -query GCF_007993965.1_ASM799396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f6d1e64-206a-4e4d-ae3c-74e060410c55/dqc_reference/reference_markers.fasta -out GCF_007993965.1_ASM799396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:57,761] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:57,764] [INFO] Selected 17 target genomes.
[2024-01-24 14:05:57,765] [INFO] Target genome list was writen to GCF_007993965.1_ASM799396v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:57,780] [INFO] Task started: fastANI
[2024-01-24 14:05:57,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgeac910a0-7f24-419f-a58d-1a8275bbd8fb/GCF_007993965.1_ASM799396v1_genomic.fna.gz --refList GCF_007993965.1_ASM799396v1_genomic.fna/target_genomes.txt --output GCF_007993965.1_ASM799396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:27,505] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:27,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f6d1e64-206a-4e4d-ae3c-74e060410c55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:27,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f6d1e64-206a-4e4d-ae3c-74e060410c55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:27,526] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:27,526] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:27,527] [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 muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	100.0	2489	2491	95	conclusive
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	99.9968	2468	2491	95	conclusive
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	82.7231	1292	2491	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	81.1441	1124	2491	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	81.1293	1142	2491	95	below_threshold
Prauserella marina	strain=DSM 45268	GCA_002240355.1	530584	530584	type	True	80.757	1120	2491	95	below_threshold
Prauserella marina	strain=DSM 45268	GCA_003182115.1	530584	530584	type	True	80.7269	1094	2491	95	below_threshold
Amycolatopsis palatopharyngis	strain=DSM 44832	GCA_003385185.1	187982	187982	type	True	80.6462	1025	2491	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.6416	1151	2491	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	80.5253	1150	2491	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	80.5185	1164	2491	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	80.3657	950	2491	95	below_threshold
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	80.3502	930	2491	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	80.3479	983	2491	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	80.3087	1148	2491	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.1839	1142	2491	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	77.9776	839	2491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:27,529] [INFO] DFAST Taxonomy check result was written to GCF_007993965.1_ASM799396v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:27,529] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:27,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:27,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f6d1e64-206a-4e4d-ae3c-74e060410c55/dqc_reference/checkm_data
[2024-01-24 14:06:27,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:27,607] [INFO] Task started: CheckM
[2024-01-24 14:06:27,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007993965.1_ASM799396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007993965.1_ASM799396v1_genomic.fna/checkm_input GCF_007993965.1_ASM799396v1_genomic.fna/checkm_result
[2024-01-24 14:08:39,051] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:39,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:39,074] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:39,074] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:39,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007993965.1_ASM799396v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:39,075] [INFO] Task started: Blastn
[2024-01-24 14:08:39,075] [INFO] Running command: blastn -query GCF_007993965.1_ASM799396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f6d1e64-206a-4e4d-ae3c-74e060410c55/dqc_reference/reference_markers_gtdb.fasta -out GCF_007993965.1_ASM799396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:41,185] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:41,190] [INFO] Selected 13 target genomes.
[2024-01-24 14:08:41,190] [INFO] Target genome list was writen to GCF_007993965.1_ASM799396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:41,225] [INFO] Task started: fastANI
[2024-01-24 14:08:41,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgeac910a0-7f24-419f-a58d-1a8275bbd8fb/GCF_007993965.1_ASM799396v1_genomic.fna.gz --refList GCF_007993965.1_ASM799396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007993965.1_ASM799396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:05,569] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:05,587] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:05,588] [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_003202285.1	s__Saccharomonospora muralis	99.9955	2470	2491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003202235.1	s__Saccharomonospora sp003202235	83.9459	1544	2491	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	83.8909	1473	2491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	82.8321	1379	2491	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	82.729	1290	2491	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	82.5662	1421	2491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	81.1154	1130	2491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001942305.1	s__Saccharomonospora sp001942305	80.7989	972	2491	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	80.7401	1121	2491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003385185.1	s__Amycolatopsis_D palatopharyngis	80.6553	1022	2491	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_000719975.1	s__Saccharomonospora rugosa	80.312	937	2491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	-
GCF_007713745.1	s__Amycolatopsis acidiphila	80.1819	1103	2491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013410405.1	s__Amycolatopsis endophytica	80.0982	1117	2491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:05,590] [INFO] GTDB search result was written to GCF_007993965.1_ASM799396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:05,591] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:05,594] [INFO] DFAST_QC result json was written to GCF_007993965.1_ASM799396v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:05,594] [INFO] DFAST_QC completed!
[2024-01-24 14:09:05,594] [INFO] Total running time: 0h3m34s