[2024-01-24 13:12:49,154] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:49,156] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:49,156] [INFO] DQC Reference Directory: /var/lib/cwl/stg58c4b49f-30ab-4fb1-9f37-6cfa38a8af44/dqc_reference
[2024-01-24 13:12:50,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:50,379] [INFO] Task started: Prodigal
[2024-01-24 13:12:50,379] [INFO] Running command: gunzip -c /var/lib/cwl/stg98d3a262-d38c-4dd2-b1fe-bc12f960cc09/GCF_011761185.1_ASM1176118v1_genomic.fna.gz | prodigal -d GCF_011761185.1_ASM1176118v1_genomic.fna/cds.fna -a GCF_011761185.1_ASM1176118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:08,766] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:08,766] [INFO] Task started: HMMsearch
[2024-01-24 13:13:08,766] [INFO] Running command: hmmsearch --tblout GCF_011761185.1_ASM1176118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58c4b49f-30ab-4fb1-9f37-6cfa38a8af44/dqc_reference/reference_markers.hmm GCF_011761185.1_ASM1176118v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:09,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:09,140] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg98d3a262-d38c-4dd2-b1fe-bc12f960cc09/GCF_011761185.1_ASM1176118v1_genomic.fna.gz]
[2024-01-24 13:13:09,195] [INFO] Query marker FASTA was written to GCF_011761185.1_ASM1176118v1_genomic.fna/markers.fasta
[2024-01-24 13:13:09,196] [INFO] Task started: Blastn
[2024-01-24 13:13:09,196] [INFO] Running command: blastn -query GCF_011761185.1_ASM1176118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58c4b49f-30ab-4fb1-9f37-6cfa38a8af44/dqc_reference/reference_markers.fasta -out GCF_011761185.1_ASM1176118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:10,475] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:10,478] [INFO] Selected 12 target genomes.
[2024-01-24 13:13:10,479] [INFO] Target genome list was writen to GCF_011761185.1_ASM1176118v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:10,485] [INFO] Task started: fastANI
[2024-01-24 13:13:10,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg98d3a262-d38c-4dd2-b1fe-bc12f960cc09/GCF_011761185.1_ASM1176118v1_genomic.fna.gz --refList GCF_011761185.1_ASM1176118v1_genomic.fna/target_genomes.txt --output GCF_011761185.1_ASM1176118v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:27,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:27,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58c4b49f-30ab-4fb1-9f37-6cfa38a8af44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:27,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58c4b49f-30ab-4fb1-9f37-6cfa38a8af44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:27,235] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:27,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:27,235] [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 amisosensis	strain=DSM 45685	GCA_011761185.1	1128677	1128677	type	True	100.0	1842	1844	95	conclusive
Saccharomonospora marina	strain=XMU15	GCA_000244955.1	632569	632569	type	True	92.6516	1633	1844	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	81.7064	1108	1844	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	81.6303	1134	1844	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.6025	905	1844	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	79.7746	797	1844	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	79.7359	800	1844	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.2981	818	1844	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.1993	777	1844	95	below_threshold
Amycolatopsis rhizosphaerae	strain=TBRC 6029	GCA_007713715.1	2053003	2053003	type	True	78.9476	637	1844	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	78.9054	677	1844	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.2398	756	1844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:27,237] [INFO] DFAST Taxonomy check result was written to GCF_011761185.1_ASM1176118v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:27,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:27,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:27,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58c4b49f-30ab-4fb1-9f37-6cfa38a8af44/dqc_reference/checkm_data
[2024-01-24 13:13:27,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:27,292] [INFO] Task started: CheckM
[2024-01-24 13:13:27,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011761185.1_ASM1176118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011761185.1_ASM1176118v1_genomic.fna/checkm_input GCF_011761185.1_ASM1176118v1_genomic.fna/checkm_result
[2024-01-24 13:14:26,708] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:26,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:26,732] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:26,733] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:26,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011761185.1_ASM1176118v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:26,733] [INFO] Task started: Blastn
[2024-01-24 13:14:26,734] [INFO] Running command: blastn -query GCF_011761185.1_ASM1176118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58c4b49f-30ab-4fb1-9f37-6cfa38a8af44/dqc_reference/reference_markers_gtdb.fasta -out GCF_011761185.1_ASM1176118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:28,556] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:28,563] [INFO] Selected 11 target genomes.
[2024-01-24 13:14:28,563] [INFO] Target genome list was writen to GCF_011761185.1_ASM1176118v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:28,572] [INFO] Task started: fastANI
[2024-01-24 13:14:28,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg98d3a262-d38c-4dd2-b1fe-bc12f960cc09/GCF_011761185.1_ASM1176118v1_genomic.fna.gz --refList GCF_011761185.1_ASM1176118v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011761185.1_ASM1176118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:44,554] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:44,565] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:44,565] [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_011761185.1	s__Saccharomonospora amisosensis	100.0	1843	1844	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_000244955.1	s__Saccharomonospora marina	92.6513	1633	1844	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	81.6759	1114	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003202235.1	s__Saccharomonospora sp003202235	81.2595	1053	1844	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	80.8051	1016	1844	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	80.7329	945	1844	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	80.625	959	1844	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	79.747	799	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004214935.1	s__Amycolatopsis suaedae	79.1201	782	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739085.1	s__Amycolatopsis methanolica	79.0752	803	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_007713715.1	s__Amycolatopsis rhizosphaerae	78.9374	640	1844	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 13:14:44,567] [INFO] GTDB search result was written to GCF_011761185.1_ASM1176118v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:44,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:44,571] [INFO] DFAST_QC result json was written to GCF_011761185.1_ASM1176118v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:44,571] [INFO] DFAST_QC completed!
[2024-01-24 13:14:44,571] [INFO] Total running time: 0h1m55s