[2024-01-24 12:45:09,806] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:09,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:09,811] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb566e78-678f-47bf-8768-d5ff640009c0/dqc_reference
[2024-01-24 12:45:13,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,084] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg8154da1c-5b40-4256-b49e-d79fc53080d8/GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/cds.fna -a GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:30,096] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:30,096] [INFO] Task started: HMMsearch
[2024-01-24 12:45:30,097] [INFO] Running command: hmmsearch --tblout GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb566e78-678f-47bf-8768-d5ff640009c0/dqc_reference/reference_markers.hmm GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:30,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:30,423] [INFO] Found 6/6 markers.
[2024-01-24 12:45:30,478] [INFO] Query marker FASTA was written to GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:45:30,478] [INFO] Task started: Blastn
[2024-01-24 12:45:30,479] [INFO] Running command: blastn -query GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb566e78-678f-47bf-8768-d5ff640009c0/dqc_reference/reference_markers.fasta -out GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:31,916] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:31,920] [INFO] Selected 21 target genomes.
[2024-01-24 12:45:31,920] [INFO] Target genome list was writen to GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:45:31,931] [INFO] Task started: fastANI
[2024-01-24 12:45:31,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg8154da1c-5b40-4256-b49e-d79fc53080d8/GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna.gz --refList GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:02,906] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:02,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb566e78-678f-47bf-8768-d5ff640009c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:02,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb566e78-678f-47bf-8768-d5ff640009c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:02,927] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:46:02,927] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:02,928] [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
Pseudonocardia thermophila	strain=DSM 43832	GCA_900142365.1	1848	1848	type	True	100.0	2005	2008	95	conclusive
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	80.4282	1000	2008	95	below_threshold
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	80.3341	1069	2008	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	80.2856	1100	2008	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	80.2	1124	2008	95	below_threshold
Pseudonocardia bannensis	strain=DSM 45300	GCA_012911875.1	630973	630973	type	True	79.8161	876	2008	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	79.8119	964	2008	95	below_threshold
Pseudonocardia acidicola	strain=K10HN5	GCA_012911935.1	2724939	2724939	type	True	79.7679	939	2008	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	79.7596	1070	2008	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	79.7238	1044	2008	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	79.7127	1081	2008	95	below_threshold
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	79.6619	933	2008	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	79.6429	1038	2008	95	below_threshold
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	77.3657	751	2008	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	77.3505	745	2008	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	77.3324	731	2008	95	below_threshold
Nocardia acididurans	strain=LPG 2	GCA_016741815.1	2802282	2802282	type	True	76.3612	470	2008	95	below_threshold
Nocardia inohanensis	strain=NBRC 100128	GCA_001612945.1	209246	209246	type	True	76.2468	439	2008	95	below_threshold
Nocardia uniformis	strain=JCM 3224	GCA_013004475.1	53432	53432	type	True	76.1571	359	2008	95	below_threshold
Nocardia uniformis	strain=NBRC 13702	GCA_001613345.1	53432	53432	type	True	76.1455	355	2008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:02,929] [INFO] DFAST Taxonomy check result was written to GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:46:02,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:02,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:02,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb566e78-678f-47bf-8768-d5ff640009c0/dqc_reference/checkm_data
[2024-01-24 12:46:02,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:02,988] [INFO] Task started: CheckM
[2024-01-24 12:46:02,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/checkm_input GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:47:28,511] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:28,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:28,544] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:28,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:28,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:47:28,545] [INFO] Task started: Blastn
[2024-01-24 12:47:28,545] [INFO] Running command: blastn -query GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb566e78-678f-47bf-8768-d5ff640009c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:30,598] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:30,601] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:30,601] [INFO] Target genome list was writen to GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:30,617] [INFO] Task started: fastANI
[2024-01-24 12:47:30,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg8154da1c-5b40-4256-b49e-d79fc53080d8/GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna.gz --refList GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:03,247] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:03,266] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:03,268] [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_900142365.1	s__Pseudonocardia thermophila	100.0	2005	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	80.4791	993	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899645.1	s__Pseudonocardia sp001899645	80.351	1024	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.47	99.47	0.91	0.91	2	-
GCA_019263585.1	s__Pseudonocardia sp019263585	80.325	1091	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.90	99.65	0.98	0.94	5	-
GCF_014235185.1	s__Pseudonocardia sp014235185	80.2453	1086	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155125.1	s__Pseudonocardia broussonetiae	80.1564	1134	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942415.1	s__Pseudonocardia sp001942415	79.9636	1033	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911875.1	s__Pseudonocardia bannensis	79.8841	864	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716445.1	s__Pseudonocardia kunmingensis	79.7525	1073	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911935.1	s__Pseudonocardia sp012911935	79.7287	946	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717045.1	s__Pseudonocardia cypriaca	79.7251	1043	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911925.1	s__Pseudonocardia xinjiangensis	79.7115	924	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994075.1	s__Pseudonocardia hierapolitana	79.7029	1084	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196675.1	s__Pseudonocardia dioxanivorans	79.657	1035	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCA_001942185.1	s__Pseudonocardia sp001942185	79.6039	1058	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141105.1	s__Saccharopolyspora_D erythraea_A	77.443	717	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	76.7826	463	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_016741815.1	s__Nocardia sp016741815	76.347	473	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613345.1	s__Nocardia uniformis	76.1418	356	2008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:03,273] [INFO] GTDB search result was written to GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:03,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:03,281] [INFO] DFAST_QC result json was written to GCF_900142365.1_IMG-taxon_2700988696_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:48:03,282] [INFO] DFAST_QC completed!
[2024-01-24 12:48:03,282] [INFO] Total running time: 0h2m53s