[2024-01-24 14:06:29,873] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,875] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg155d48c1-3c84-472c-9e39-d50d17f6164a/dqc_reference
[2024-01-24 14:06:31,259] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,261] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f1d0bea-a8bc-4199-85ff-544224c95fed/GCF_003202235.1_ASM320223v1_genomic.fna.gz | prodigal -d GCF_003202235.1_ASM320223v1_genomic.fna/cds.fna -a GCF_003202235.1_ASM320223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:56,258] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:56,258] [INFO] Task started: HMMsearch
[2024-01-24 14:06:56,259] [INFO] Running command: hmmsearch --tblout GCF_003202235.1_ASM320223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg155d48c1-3c84-472c-9e39-d50d17f6164a/dqc_reference/reference_markers.hmm GCF_003202235.1_ASM320223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:56,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:56,612] [INFO] Found 6/6 markers.
[2024-01-24 14:06:56,675] [INFO] Query marker FASTA was written to GCF_003202235.1_ASM320223v1_genomic.fna/markers.fasta
[2024-01-24 14:06:56,675] [INFO] Task started: Blastn
[2024-01-24 14:06:56,675] [INFO] Running command: blastn -query GCF_003202235.1_ASM320223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155d48c1-3c84-472c-9e39-d50d17f6164a/dqc_reference/reference_markers.fasta -out GCF_003202235.1_ASM320223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:58,085] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:58,088] [INFO] Selected 20 target genomes.
[2024-01-24 14:06:58,088] [INFO] Target genome list was writen to GCF_003202235.1_ASM320223v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:58,098] [INFO] Task started: fastANI
[2024-01-24 14:06:58,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f1d0bea-a8bc-4199-85ff-544224c95fed/GCF_003202235.1_ASM320223v1_genomic.fna.gz --refList GCF_003202235.1_ASM320223v1_genomic.fna/target_genomes.txt --output GCF_003202235.1_ASM320223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:30,078] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:30,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg155d48c1-3c84-472c-9e39-d50d17f6164a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:30,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg155d48c1-3c84-472c-9e39-d50d17f6164a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:30,095] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:07:30,096] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:07:30,096] [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	86.1916	1656	2680	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	84.0117	1528	2680	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	83.9654	1518	2680	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	80.8848	1205	2680	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	80.8777	1218	2680	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	80.8614	1191	2680	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.7453	1165	2680	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	80.6404	1121	2680	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	80.6243	1134	2680	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	80.5304	988	2680	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	80.4653	1172	2680	95	below_threshold
Saccharomonospora cyanea	strain=NA-134	GCA_000244975.1	40989	40989	type	True	80.458	958	2680	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	80.3885	1019	2680	95	below_threshold
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	80.3501	1132	2680	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.3306	1164	2680	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.8935	1119	2680	95	below_threshold
Amycolatopsis acidicola	strain=K81G1	GCA_007713735.2	2596893	2596893	type	True	79.8906	1183	2680	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	79.5542	1152	2680	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	79.4957	1157	2680	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	79.4611	1248	2680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:30,098] [INFO] DFAST Taxonomy check result was written to GCF_003202235.1_ASM320223v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:30,099] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:30,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:30,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg155d48c1-3c84-472c-9e39-d50d17f6164a/dqc_reference/checkm_data
[2024-01-24 14:07:30,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:30,171] [INFO] Task started: CheckM
[2024-01-24 14:07:30,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003202235.1_ASM320223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003202235.1_ASM320223v1_genomic.fna/checkm_input GCF_003202235.1_ASM320223v1_genomic.fna/checkm_result
[2024-01-24 14:08:58,469] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:58,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:58,491] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:58,491] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:58,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003202235.1_ASM320223v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:58,492] [INFO] Task started: Blastn
[2024-01-24 14:08:58,492] [INFO] Running command: blastn -query GCF_003202235.1_ASM320223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155d48c1-3c84-472c-9e39-d50d17f6164a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003202235.1_ASM320223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:09:00,747] [INFO] Task succeeded: Blastn
[2024-01-24 14:09:00,751] [INFO] Selected 11 target genomes.
[2024-01-24 14:09:00,751] [INFO] Target genome list was writen to GCF_003202235.1_ASM320223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:09:00,758] [INFO] Task started: fastANI
[2024-01-24 14:09:00,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f1d0bea-a8bc-4199-85ff-544224c95fed/GCF_003202235.1_ASM320223v1_genomic.fna.gz --refList GCF_003202235.1_ASM320223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003202235.1_ASM320223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:20,999] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:21,012] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:21,013] [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_003202235.1	s__Saccharomonospora sp003202235	100.0	2672	2680	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_005146945.1	s__Saccharomonospora endophytica	92.83	2089	2680	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_016595675.1	s__Saccharomonospora sp016595675	86.2184	1652	2680	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	84.0024	1525	2680	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	82.2691	1277	2680	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	82.0919	1270	2680	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012328925.1	s__Amycolatopsis acididurans	80.8593	1191	2680	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385215.1	s__Amycolatopsis thermalba	80.716	1171	2680	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	80.6696	1269	2680	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	80.6284	1122	2680	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007713745.1	s__Amycolatopsis acidiphila	80.3398	1135	2680	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 14:09:21,016] [INFO] GTDB search result was written to GCF_003202235.1_ASM320223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:21,016] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:21,020] [INFO] DFAST_QC result json was written to GCF_003202235.1_ASM320223v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:21,021] [INFO] DFAST_QC completed!
[2024-01-24 14:09:21,021] [INFO] Total running time: 0h2m51s