[2024-01-24 12:22:28,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:28,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:28,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c538b3d-e82b-42a5-aea6-1817efd56d2e/dqc_reference
[2024-01-24 12:22:29,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,847] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,848] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5926ec6-afa0-425c-b408-ecaae39d5c18/GCF_005146945.1_ASM514694v1_genomic.fna.gz | prodigal -d GCF_005146945.1_ASM514694v1_genomic.fna/cds.fna -a GCF_005146945.1_ASM514694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:53,136] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:53,136] [INFO] Task started: HMMsearch
[2024-01-24 12:22:53,136] [INFO] Running command: hmmsearch --tblout GCF_005146945.1_ASM514694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c538b3d-e82b-42a5-aea6-1817efd56d2e/dqc_reference/reference_markers.hmm GCF_005146945.1_ASM514694v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:53,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:53,556] [INFO] Found 6/6 markers.
[2024-01-24 12:22:53,624] [INFO] Query marker FASTA was written to GCF_005146945.1_ASM514694v1_genomic.fna/markers.fasta
[2024-01-24 12:22:53,624] [INFO] Task started: Blastn
[2024-01-24 12:22:53,624] [INFO] Running command: blastn -query GCF_005146945.1_ASM514694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c538b3d-e82b-42a5-aea6-1817efd56d2e/dqc_reference/reference_markers.fasta -out GCF_005146945.1_ASM514694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:55,116] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:55,122] [INFO] Selected 24 target genomes.
[2024-01-24 12:22:55,123] [INFO] Target genome list was writen to GCF_005146945.1_ASM514694v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:55,137] [INFO] Task started: fastANI
[2024-01-24 12:22:55,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5926ec6-afa0-425c-b408-ecaae39d5c18/GCF_005146945.1_ASM514694v1_genomic.fna.gz --refList GCF_005146945.1_ASM514694v1_genomic.fna/target_genomes.txt --output GCF_005146945.1_ASM514694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:32,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:32,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c538b3d-e82b-42a5-aea6-1817efd56d2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:32,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c538b3d-e82b-42a5-aea6-1817efd56d2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:32,456] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:32,456] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:32,457] [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	85.9581	1589	2592	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	83.8746	1496	2592	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	83.8464	1519	2592	95	below_threshold
Saccharomonospora marina	strain=XMU15	GCA_000244955.1	632569	632569	type	True	81.1335	1076	2592	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	80.7984	1084	2592	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	80.7697	1089	2592	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	80.5821	1124	2592	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.4982	1151	2592	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	80.484	1191	2592	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	80.4734	957	2592	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	80.4485	950	2592	95	below_threshold
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	80.4109	1091	2592	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.358	1137	2592	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	80.3209	1208	2592	95	below_threshold
Saccharomonospora iraqiensis subsp. paurometabolica	strain=YIM 90007	GCA_000231035.3	208085	52698	type	True	80.0841	817	2592	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.7845	1097	2592	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	79.6162	1188	2592	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	79.3568	1147	2592	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	79.2974	1002	2592	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	78.3049	728	2592	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	78.2043	749	2592	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	78.1588	773	2592	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.0835	747	2592	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	78.0505	879	2592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:32,459] [INFO] DFAST Taxonomy check result was written to GCF_005146945.1_ASM514694v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:32,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:32,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:32,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c538b3d-e82b-42a5-aea6-1817efd56d2e/dqc_reference/checkm_data
[2024-01-24 12:23:32,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:32,535] [INFO] Task started: CheckM
[2024-01-24 12:23:32,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005146945.1_ASM514694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005146945.1_ASM514694v1_genomic.fna/checkm_input GCF_005146945.1_ASM514694v1_genomic.fna/checkm_result
[2024-01-24 12:24:50,768] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:50,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:50,796] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:50,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:50,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005146945.1_ASM514694v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:50,797] [INFO] Task started: Blastn
[2024-01-24 12:24:50,797] [INFO] Running command: blastn -query GCF_005146945.1_ASM514694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c538b3d-e82b-42a5-aea6-1817efd56d2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_005146945.1_ASM514694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:52,832] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:52,836] [INFO] Selected 14 target genomes.
[2024-01-24 12:24:52,836] [INFO] Target genome list was writen to GCF_005146945.1_ASM514694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:52,852] [INFO] Task started: fastANI
[2024-01-24 12:24:52,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5926ec6-afa0-425c-b408-ecaae39d5c18/GCF_005146945.1_ASM514694v1_genomic.fna.gz --refList GCF_005146945.1_ASM514694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005146945.1_ASM514694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:16,740] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:16,757] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:16,757] [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_005146945.1	s__Saccharomonospora endophytica	100.0	2590	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	conclusive
GCF_003202235.1	s__Saccharomonospora sp003202235	92.8701	2080	2592	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	85.9683	1588	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	83.8805	1513	2592	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	82.0588	1258	2592	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	81.9269	1275	2592	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	80.755	1092	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012328925.1	s__Amycolatopsis acididurans	80.5999	1123	2592	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	80.3782	1095	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000739085.1	s__Amycolatopsis methanolica	80.3409	1204	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_016907695.1	s__Actinokineospora baliensis	78.3435	722	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111175.1	s__Actinokineospora terrae	78.2087	748	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_000374445.1	s__Actinokineospora enzanensis	78.0237	755	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940455.1	s__Actinokineospora bangkokensis	78.0201	889	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:16,758] [INFO] GTDB search result was written to GCF_005146945.1_ASM514694v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:16,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:16,763] [INFO] DFAST_QC result json was written to GCF_005146945.1_ASM514694v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:16,763] [INFO] DFAST_QC completed!
[2024-01-24 12:25:16,763] [INFO] Total running time: 0h2m48s