[2024-01-25 19:45:35,868] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:35,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:35,870] [INFO] DQC Reference Directory: /var/lib/cwl/stg518b92f7-8124-4941-a82a-9eb1a87de2ab/dqc_reference
[2024-01-25 19:45:37,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:37,018] [INFO] Task started: Prodigal
[2024-01-25 19:45:37,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg66a52b82-3363-48bb-ae61-298538272733/GCF_026153295.1_ASM2615329v1_genomic.fna.gz | prodigal -d GCF_026153295.1_ASM2615329v1_genomic.fna/cds.fna -a GCF_026153295.1_ASM2615329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:47,589] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:47,589] [INFO] Task started: HMMsearch
[2024-01-25 19:45:47,589] [INFO] Running command: hmmsearch --tblout GCF_026153295.1_ASM2615329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg518b92f7-8124-4941-a82a-9eb1a87de2ab/dqc_reference/reference_markers.hmm GCF_026153295.1_ASM2615329v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:47,796] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:47,798] [INFO] Found 6/6 markers.
[2024-01-25 19:45:47,829] [INFO] Query marker FASTA was written to GCF_026153295.1_ASM2615329v1_genomic.fna/markers.fasta
[2024-01-25 19:45:47,830] [INFO] Task started: Blastn
[2024-01-25 19:45:47,830] [INFO] Running command: blastn -query GCF_026153295.1_ASM2615329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg518b92f7-8124-4941-a82a-9eb1a87de2ab/dqc_reference/reference_markers.fasta -out GCF_026153295.1_ASM2615329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:49,070] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:49,073] [INFO] Selected 27 target genomes.
[2024-01-25 19:45:49,073] [INFO] Target genome list was writen to GCF_026153295.1_ASM2615329v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:49,126] [INFO] Task started: fastANI
[2024-01-25 19:45:49,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg66a52b82-3363-48bb-ae61-298538272733/GCF_026153295.1_ASM2615329v1_genomic.fna.gz --refList GCF_026153295.1_ASM2615329v1_genomic.fna/target_genomes.txt --output GCF_026153295.1_ASM2615329v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:20,008] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:20,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg518b92f7-8124-4941-a82a-9eb1a87de2ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:20,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg518b92f7-8124-4941-a82a-9eb1a87de2ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:20,025] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:46:20,026] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:46:20,026] [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
Rhodococcus tukisamuensis	strain=JCM 11308	GCA_900101735.1	168276	168276	type	True	78.2884	450	1314	95	below_threshold
Rhodococcus tukisamuensis	strain=NBRC 100609	GCA_001894985.1	168276	168276	type	True	78.2546	450	1314	95	below_threshold
Rhodococcus maanshanensis	strain=NBRC 100610	GCA_001894865.1	183556	183556	type	True	78.1232	408	1314	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	78.1072	405	1314	95	below_threshold
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	78.0509	424	1314	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	77.9028	421	1314	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	77.9015	389	1314	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	77.8707	380	1314	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	77.8294	377	1314	95	below_threshold
Mycolicibacterium brumae	strain=DSM 44177	GCA_004014795.1	85968	85968	type	True	77.752	366	1314	95	below_threshold
Nocardia caishijiensis	strain=DSM 44831	GCA_009858255.1	184756	184756	type	True	77.6769	350	1314	95	below_threshold
Nocardia caishijiensis	strain=NBRC 108228	GCA_001612825.1	184756	184756	type	True	77.6322	356	1314	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	77.6092	475	1314	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	77.5999	475	1314	95	below_threshold
Nocardia tengchongensis	strain=CFH S0057	GCA_018362975.1	2055889	2055889	type	True	77.5833	404	1314	95	below_threshold
Williamsia maris	strain=DSM 44693	GCA_024171815.1	72806	72806	type	True	77.5754	350	1314	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	77.5398	536	1314	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	77.5074	454	1314	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	77.4929	466	1314	95	below_threshold
Nocardia cyriacigeorgica	strain=DSM 44484	GCA_005863225.1	135487	135487	type	True	77.4217	368	1314	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	77.4165	535	1314	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	77.2999	520	1314	95	below_threshold
Nocardia alba	strain=DSM 44684	GCA_004339125.1	225051	225051	type	True	77.2332	371	1314	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	77.2301	488	1314	95	below_threshold
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	77.1502	428	1314	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	77.1093	574	1314	95	below_threshold
Actinomycetospora succinea	strain=DSM 45775	GCA_004363095.1	663603	663603	type	True	77.0728	554	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:20,034] [INFO] DFAST Taxonomy check result was written to GCF_026153295.1_ASM2615329v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:20,034] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:20,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:20,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg518b92f7-8124-4941-a82a-9eb1a87de2ab/dqc_reference/checkm_data
[2024-01-25 19:46:20,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:20,078] [INFO] Task started: CheckM
[2024-01-25 19:46:20,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026153295.1_ASM2615329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026153295.1_ASM2615329v1_genomic.fna/checkm_input GCF_026153295.1_ASM2615329v1_genomic.fna/checkm_result
[2024-01-25 19:47:57,699] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:57,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:57,715] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:57,716] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:57,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026153295.1_ASM2615329v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:57,716] [INFO] Task started: Blastn
[2024-01-25 19:47:57,717] [INFO] Running command: blastn -query GCF_026153295.1_ASM2615329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg518b92f7-8124-4941-a82a-9eb1a87de2ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_026153295.1_ASM2615329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:59,658] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:59,660] [INFO] Selected 23 target genomes.
[2024-01-25 19:47:59,661] [INFO] Target genome list was writen to GCF_026153295.1_ASM2615329v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:59,686] [INFO] Task started: fastANI
[2024-01-25 19:47:59,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg66a52b82-3363-48bb-ae61-298538272733/GCF_026153295.1_ASM2615329v1_genomic.fna.gz --refList GCF_026153295.1_ASM2615329v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026153295.1_ASM2615329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:27,130] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:27,144] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:48:27,144] [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_004006015.1	s__X156 sp004006015	80.6685	595	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__X156	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882745.1	s__X156 sp017882745	78.6674	320	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__X156	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894985.1	s__Rhodococcus tukisamuensis	78.2801	447	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001894865.1	s__Rhodococcus maanshanensis	78.1053	410	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.18	96.37	0.94	0.89	3	-
GCF_006704125.1	s__Rhodococcus sp006704125	78.0672	422	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005049235.1	s__Rhodococcus oryzae	77.871	425	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.56	95.24	0.93	0.92	5	-
GCF_014126825.1	s__Tomitella sp014126825	77.8661	368	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	97.57	97.57	0.88	0.88	2	-
GCF_010726955.1	s__Mycobacterium fallax	77.8588	393	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_004014795.1	s__Mycobacterium brumae	77.7794	363	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.98	0.98	0.98	3	-
GCA_014138725.1	s__Kutzneria viridogrisea	77.6912	542	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	99.33	99.33	0.95	0.95	2	-
GCF_002155965.1	s__Allokutzneria sp002155965	77.6357	442	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allokutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	77.6063	476	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612825.1	s__Nocardia caishijiensis	77.5833	363	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018362975.1	s__Nocardia tengchongensis	77.5657	408	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203355.1	s__Kutzneria kofuensis	77.5332	530	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	77.4941	456	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	77.44	532	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477355.1	s__Nocardia blacklockiae	77.4123	458	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	77.3479	511	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014360565.1	s__Nocardia sp014360565	77.2934	289	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620785.1	s__Pseudonocardia acaciae	77.1258	569	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363095.1	s__Actinomycetospora succinea	77.0977	549	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	77.0769	483	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:27,145] [INFO] GTDB search result was written to GCF_026153295.1_ASM2615329v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:27,146] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:27,150] [INFO] DFAST_QC result json was written to GCF_026153295.1_ASM2615329v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:27,150] [INFO] DFAST_QC completed!
[2024-01-25 19:48:27,150] [INFO] Total running time: 0h2m51s