[2024-01-25 19:58:35,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:35,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:35,569] [INFO] DQC Reference Directory: /var/lib/cwl/stgfee52238-e0e0-49ad-b23c-78c1ac5a487c/dqc_reference
[2024-01-25 19:58:36,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:36,675] [INFO] Task started: Prodigal
[2024-01-25 19:58:36,675] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc9d83bc-7f9d-47eb-aa41-2a5e92b5c324/GCF_000220945.1_ASM22094v1_genomic.fna.gz | prodigal -d GCF_000220945.1_ASM22094v1_genomic.fna/cds.fna -a GCF_000220945.1_ASM22094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:07,406] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:07,406] [INFO] Task started: HMMsearch
[2024-01-25 19:59:07,406] [INFO] Running command: hmmsearch --tblout GCF_000220945.1_ASM22094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfee52238-e0e0-49ad-b23c-78c1ac5a487c/dqc_reference/reference_markers.hmm GCF_000220945.1_ASM22094v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:07,950] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:07,951] [INFO] Found 6/6 markers.
[2024-01-25 19:59:08,024] [INFO] Query marker FASTA was written to GCF_000220945.1_ASM22094v1_genomic.fna/markers.fasta
[2024-01-25 19:59:08,025] [INFO] Task started: Blastn
[2024-01-25 19:59:08,025] [INFO] Running command: blastn -query GCF_000220945.1_ASM22094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee52238-e0e0-49ad-b23c-78c1ac5a487c/dqc_reference/reference_markers.fasta -out GCF_000220945.1_ASM22094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:09,297] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:09,300] [INFO] Selected 18 target genomes.
[2024-01-25 19:59:09,300] [INFO] Target genome list was writen to GCF_000220945.1_ASM22094v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:09,314] [INFO] Task started: fastANI
[2024-01-25 19:59:09,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc9d83bc-7f9d-47eb-aa41-2a5e92b5c324/GCF_000220945.1_ASM22094v1_genomic.fna.gz --refList GCF_000220945.1_ASM22094v1_genomic.fna/target_genomes.txt --output GCF_000220945.1_ASM22094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:55,376] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:55,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfee52238-e0e0-49ad-b23c-78c1ac5a487c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:55,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfee52238-e0e0-49ad-b23c-78c1ac5a487c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:55,388] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:55,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:55,388] [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
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	100.0	3411	3412	95	conclusive
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	92.0807	2291	3412	95	below_threshold
Amycolatopsis rifamycinica	strain=DSM 46095	GCA_000695625.1	287986	287986	type	True	91.7421	2437	3412	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	91.1653	2555	3412	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	90.8699	2528	3412	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	90.7064	2080	3412	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	90.3655	2530	3412	95	below_threshold
Amycolatopsis balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	89.9945	2546	3412	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	88.9715	2481	3412	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	88.8098	2180	3412	95	below_threshold
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	88.8077	2409	3412	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	88.7399	2456	3412	95	below_threshold
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	88.7203	2211	3412	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	80.7959	1419	3412	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.1776	1236	3412	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.1531	1115	3412	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	78.6984	789	3412	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.5684	1097	3412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:55,390] [INFO] DFAST Taxonomy check result was written to GCF_000220945.1_ASM22094v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:55,390] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:55,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:55,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfee52238-e0e0-49ad-b23c-78c1ac5a487c/dqc_reference/checkm_data
[2024-01-25 19:59:55,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:55,480] [INFO] Task started: CheckM
[2024-01-25 19:59:55,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000220945.1_ASM22094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000220945.1_ASM22094v1_genomic.fna/checkm_input GCF_000220945.1_ASM22094v1_genomic.fna/checkm_result
[2024-01-25 20:03:27,008] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:27,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:27,043] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:27,043] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:27,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000220945.1_ASM22094v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:27,044] [INFO] Task started: Blastn
[2024-01-25 20:03:27,044] [INFO] Running command: blastn -query GCF_000220945.1_ASM22094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee52238-e0e0-49ad-b23c-78c1ac5a487c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000220945.1_ASM22094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:29,138] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:29,141] [INFO] Selected 12 target genomes.
[2024-01-25 20:03:29,141] [INFO] Target genome list was writen to GCF_000220945.1_ASM22094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:29,156] [INFO] Task started: fastANI
[2024-01-25 20:03:29,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc9d83bc-7f9d-47eb-aa41-2a5e92b5c324/GCF_000220945.1_ASM22094v1_genomic.fna.gz --refList GCF_000220945.1_ASM22094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000220945.1_ASM22094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:06,344] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:06,352] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:06,352] [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_000220945.1	s__Amycolatopsis mediterranei	100.0	3411	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	conclusive
GCF_002904335.1	s__Amycolatopsis sp002904335	94.2377	2669	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155975.1	s__Amycolatopsis kentuckyensis	92.05	2295	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654205.1	s__Amycolatopsis bullii	91.9871	2488	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695625.1	s__Amycolatopsis rifamycinica	91.7511	2436	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308975.1	s__Amycolatopsis sp017308975	91.2147	2500	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364075.1	s__Amycolatopsis sp013364075	91.1158	2605	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	90.8506	2531	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002904295.1	s__Amycolatopsis sp002904295	90.6791	2475	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234595.1	s__Amycolatopsis vastitatis	90.3837	2527	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384295.1	s__Amycolatopsis balhimycina	90.0043	2545	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900107925.1	s__Amycolatopsis pretoriensis	88.7987	2411	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:06,354] [INFO] GTDB search result was written to GCF_000220945.1_ASM22094v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:06,354] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:06,357] [INFO] DFAST_QC result json was written to GCF_000220945.1_ASM22094v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:06,358] [INFO] DFAST_QC completed!
[2024-01-25 20:04:06,358] [INFO] Total running time: 0h5m31s