[2024-01-24 14:38:45,566] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ccbe6ad-1df0-4997-a913-08ac77ae97f5/dqc_reference
[2024-01-24 14:38:48,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,293] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,294] [INFO] Running command: gunzip -c /var/lib/cwl/stg8144bbae-96de-4054-8be8-bbca45a9f057/GCF_017875555.1_ASM1787555v1_genomic.fna.gz | prodigal -d GCF_017875555.1_ASM1787555v1_genomic.fna/cds.fna -a GCF_017875555.1_ASM1787555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:25,569] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:25,569] [INFO] Task started: HMMsearch
[2024-01-24 14:39:25,569] [INFO] Running command: hmmsearch --tblout GCF_017875555.1_ASM1787555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ccbe6ad-1df0-4997-a913-08ac77ae97f5/dqc_reference/reference_markers.hmm GCF_017875555.1_ASM1787555v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:26,008] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:26,010] [INFO] Found 6/6 markers.
[2024-01-24 14:39:26,089] [INFO] Query marker FASTA was written to GCF_017875555.1_ASM1787555v1_genomic.fna/markers.fasta
[2024-01-24 14:39:26,090] [INFO] Task started: Blastn
[2024-01-24 14:39:26,090] [INFO] Running command: blastn -query GCF_017875555.1_ASM1787555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ccbe6ad-1df0-4997-a913-08ac77ae97f5/dqc_reference/reference_markers.fasta -out GCF_017875555.1_ASM1787555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:27,564] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:27,569] [INFO] Selected 24 target genomes.
[2024-01-24 14:39:27,570] [INFO] Target genome list was writen to GCF_017875555.1_ASM1787555v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:27,579] [INFO] Task started: fastANI
[2024-01-24 14:39:27,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg8144bbae-96de-4054-8be8-bbca45a9f057/GCF_017875555.1_ASM1787555v1_genomic.fna.gz --refList GCF_017875555.1_ASM1787555v1_genomic.fna/target_genomes.txt --output GCF_017875555.1_ASM1787555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:20,787] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:20,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ccbe6ad-1df0-4997-a913-08ac77ae97f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:20,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ccbe6ad-1df0-4997-a913-08ac77ae97f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:20,809] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:20,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:20,810] [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 magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	100.0	3146	3147	95	conclusive
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	88.9277	2307	3147	95	below_threshold
Amycolatopsis suaedae	strain=8-3EHSu	GCA_004214935.1	2510978	2510978	type	True	81.1761	1470	3147	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	80.5557	1513	3147	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.3991	1275	3147	95	below_threshold
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	80.2973	1189	3147	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	80.2843	1404	3147	95	below_threshold
Amycolatopsis japonica	strain=MG417-CF17	GCA_000732925.1	208439	208439	type	True	80.2648	1407	3147	95	below_threshold
Amycolatopsis roodepoortensis	strain=DSM 46661	GCA_014873915.1	700274	700274	type	True	80.2616	1395	3147	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.2581	1231	3147	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	80.1701	1371	3147	95	below_threshold
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	80.1626	1527	3147	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	80.1622	1307	3147	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	80.1533	1588	3147	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001558125.2	546365	546365	type	True	80.134	1307	3147	95	below_threshold
Amycolatopsis regifaucium	strain=DSM 45072	GCA_900113515.1	546365	546365	type	True	80.1291	1320	3147	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001613935.1	546365	546365	type	True	80.1245	1305	3147	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	80.01	1570	3147	95	below_threshold
Amycolatopsis acidicola	strain=K81G1	GCA_007713735.2	2596893	2596893	type	True	79.8677	1150	3147	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.8348	1249	3147	95	below_threshold
Amycolatopsis circi	strain=DSM 45561	GCA_003385235.1	871959	871959	type	True	79.6975	1226	3147	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.6895	1157	3147	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	79.6893	1124	3147	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.3652	987	3147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:20,812] [INFO] DFAST Taxonomy check result was written to GCF_017875555.1_ASM1787555v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:20,812] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:20,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:20,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ccbe6ad-1df0-4997-a913-08ac77ae97f5/dqc_reference/checkm_data
[2024-01-24 14:40:20,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:20,904] [INFO] Task started: CheckM
[2024-01-24 14:40:20,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017875555.1_ASM1787555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017875555.1_ASM1787555v1_genomic.fna/checkm_input GCF_017875555.1_ASM1787555v1_genomic.fna/checkm_result
[2024-01-24 14:43:19,922] [INFO] Task succeeded: CheckM
[2024-01-24 14:43:19,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:43:19,950] [INFO] ===== Completeness check finished =====
[2024-01-24 14:43:19,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:43:19,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017875555.1_ASM1787555v1_genomic.fna/markers.fasta)
[2024-01-24 14:43:19,951] [INFO] Task started: Blastn
[2024-01-24 14:43:19,951] [INFO] Running command: blastn -query GCF_017875555.1_ASM1787555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ccbe6ad-1df0-4997-a913-08ac77ae97f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_017875555.1_ASM1787555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:43:22,060] [INFO] Task succeeded: Blastn
[2024-01-24 14:43:22,070] [INFO] Selected 11 target genomes.
[2024-01-24 14:43:22,070] [INFO] Target genome list was writen to GCF_017875555.1_ASM1787555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:43:22,078] [INFO] Task started: fastANI
[2024-01-24 14:43:22,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg8144bbae-96de-4054-8be8-bbca45a9f057/GCF_017875555.1_ASM1787555v1_genomic.fna.gz --refList GCF_017875555.1_ASM1787555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017875555.1_ASM1787555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:54,539] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:54,554] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:43:54,554] [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_017875555.1	s__Amycolatopsis magusensis	100.0	3146	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009429145.1	s__Amycolatopsis sp009429145	89.2869	2456	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309385.1	s__Amycolatopsis sp017309385	89.1169	2452	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	88.9048	2310	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214935.1	s__Amycolatopsis suaedae	81.1509	1476	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	80.5935	1504	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653945.1	s__Amycolatopsis deserti	80.497	1274	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110575.1	s__Amycolatopsis saalfeldensis	80.2775	1406	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234405.1	s__Amycolatopsis thailandensis	80.1681	1307	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613935.1	s__Amycolatopsis regifaucium	80.1113	1309	3147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900105945.1	s__Amycolatopsis tolypomycina	79.9966	1576	3147	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 14:43:54,557] [INFO] GTDB search result was written to GCF_017875555.1_ASM1787555v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:54,557] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:54,562] [INFO] DFAST_QC result json was written to GCF_017875555.1_ASM1787555v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:54,562] [INFO] DFAST_QC completed!
[2024-01-24 14:43:54,562] [INFO] Total running time: 0h5m9s