[2024-01-25 18:59:05,481] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:05,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:05,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9deadc6-854b-48a0-9af1-5ca133265496/dqc_reference
[2024-01-25 18:59:06,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:06,614] [INFO] Task started: Prodigal
[2024-01-25 18:59:06,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg25488069-c09e-4b23-bc8c-875d215ddeff/GCF_026017845.1_ASM2601784v1_genomic.fna.gz | prodigal -d GCF_026017845.1_ASM2601784v1_genomic.fna/cds.fna -a GCF_026017845.1_ASM2601784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:37,243] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:37,244] [INFO] Task started: HMMsearch
[2024-01-25 18:59:37,244] [INFO] Running command: hmmsearch --tblout GCF_026017845.1_ASM2601784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9deadc6-854b-48a0-9af1-5ca133265496/dqc_reference/reference_markers.hmm GCF_026017845.1_ASM2601784v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:37,653] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:37,654] [INFO] Found 6/6 markers.
[2024-01-25 18:59:37,730] [INFO] Query marker FASTA was written to GCF_026017845.1_ASM2601784v1_genomic.fna/markers.fasta
[2024-01-25 18:59:37,730] [INFO] Task started: Blastn
[2024-01-25 18:59:37,730] [INFO] Running command: blastn -query GCF_026017845.1_ASM2601784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9deadc6-854b-48a0-9af1-5ca133265496/dqc_reference/reference_markers.fasta -out GCF_026017845.1_ASM2601784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:38,993] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:38,996] [INFO] Selected 18 target genomes.
[2024-01-25 18:59:38,997] [INFO] Target genome list was writen to GCF_026017845.1_ASM2601784v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:39,010] [INFO] Task started: fastANI
[2024-01-25 18:59:39,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg25488069-c09e-4b23-bc8c-875d215ddeff/GCF_026017845.1_ASM2601784v1_genomic.fna.gz --refList GCF_026017845.1_ASM2601784v1_genomic.fna/target_genomes.txt --output GCF_026017845.1_ASM2601784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:26,017] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:26,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9deadc6-854b-48a0-9af1-5ca133265496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:26,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9deadc6-854b-48a0-9af1-5ca133265496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:26,029] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:00:26,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:26,030] [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	99.9708	3401	3535	95	conclusive
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	92.1377	2279	3535	95	below_threshold
Amycolatopsis rifamycinica	strain=DSM 46095	GCA_000695625.1	287986	287986	type	True	91.7716	2447	3535	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	91.1596	2547	3535	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	90.8093	2549	3535	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	90.6704	2097	3535	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	90.4223	2534	3535	95	below_threshold
Amycolatopsis balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	89.9293	2542	3535	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	88.9442	2487	3535	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	88.8798	2175	3535	95	below_threshold
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	88.7416	2431	3535	95	below_threshold
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	88.6862	2225	3535	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	88.6546	2479	3535	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	80.7984	1432	3535	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.1053	1254	3535	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.0525	1133	3535	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	78.5906	805	3535	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.5127	1109	3535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:26,031] [INFO] DFAST Taxonomy check result was written to GCF_026017845.1_ASM2601784v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:26,031] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:26,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:26,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9deadc6-854b-48a0-9af1-5ca133265496/dqc_reference/checkm_data
[2024-01-25 19:00:26,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:26,124] [INFO] Task started: CheckM
[2024-01-25 19:00:26,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026017845.1_ASM2601784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026017845.1_ASM2601784v1_genomic.fna/checkm_input GCF_026017845.1_ASM2601784v1_genomic.fna/checkm_result
[2024-01-25 19:03:27,512] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:27,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:27,545] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:27,546] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:27,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026017845.1_ASM2601784v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:27,547] [INFO] Task started: Blastn
[2024-01-25 19:03:27,547] [INFO] Running command: blastn -query GCF_026017845.1_ASM2601784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9deadc6-854b-48a0-9af1-5ca133265496/dqc_reference/reference_markers_gtdb.fasta -out GCF_026017845.1_ASM2601784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:29,572] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:29,574] [INFO] Selected 12 target genomes.
[2024-01-25 19:03:29,574] [INFO] Target genome list was writen to GCF_026017845.1_ASM2601784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:29,594] [INFO] Task started: fastANI
[2024-01-25 19:03:29,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg25488069-c09e-4b23-bc8c-875d215ddeff/GCF_026017845.1_ASM2601784v1_genomic.fna.gz --refList GCF_026017845.1_ASM2601784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026017845.1_ASM2601784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:07,125] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:07,134] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:07,134] [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	99.9644	3403	3535	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	94.2421	2660	3535	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	92.1723	2273	3535	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	92.0499	2454	3535	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	91.7915	2444	3535	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	91.2197	2499	3535	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	91.1758	2598	3535	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	90.7956	2551	3535	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	90.6867	2479	3535	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	90.4673	2527	3535	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	89.9396	2540	3535	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	88.7329	2432	3535	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 19:04:07,136] [INFO] GTDB search result was written to GCF_026017845.1_ASM2601784v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:07,137] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:07,141] [INFO] DFAST_QC result json was written to GCF_026017845.1_ASM2601784v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:07,141] [INFO] DFAST_QC completed!
[2024-01-25 19:04:07,141] [INFO] Total running time: 0h5m2s