[2024-01-24 10:57:26,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c7b705f-48c3-464c-ac32-26966aadf5fa/dqc_reference
[2024-01-24 10:57:27,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:27,906] [INFO] Task started: Prodigal
[2024-01-24 10:57:27,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg37f2d6b4-4228-4cd7-818b-69ea462f698a/GCF_004339565.1_ASM433956v1_genomic.fna.gz | prodigal -d GCF_004339565.1_ASM433956v1_genomic.fna/cds.fna -a GCF_004339565.1_ASM433956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:48,543] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:48,544] [INFO] Task started: HMMsearch
[2024-01-24 10:57:48,544] [INFO] Running command: hmmsearch --tblout GCF_004339565.1_ASM433956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c7b705f-48c3-464c-ac32-26966aadf5fa/dqc_reference/reference_markers.hmm GCF_004339565.1_ASM433956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:48,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:48,923] [INFO] Found 6/6 markers.
[2024-01-24 10:57:48,981] [INFO] Query marker FASTA was written to GCF_004339565.1_ASM433956v1_genomic.fna/markers.fasta
[2024-01-24 10:57:48,982] [INFO] Task started: Blastn
[2024-01-24 10:57:48,982] [INFO] Running command: blastn -query GCF_004339565.1_ASM433956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c7b705f-48c3-464c-ac32-26966aadf5fa/dqc_reference/reference_markers.fasta -out GCF_004339565.1_ASM433956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:50,363] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:50,366] [INFO] Selected 14 target genomes.
[2024-01-24 10:57:50,366] [INFO] Target genome list was writen to GCF_004339565.1_ASM433956v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:50,371] [INFO] Task started: fastANI
[2024-01-24 10:57:50,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg37f2d6b4-4228-4cd7-818b-69ea462f698a/GCF_004339565.1_ASM433956v1_genomic.fna.gz --refList GCF_004339565.1_ASM433956v1_genomic.fna/target_genomes.txt --output GCF_004339565.1_ASM433956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:16,607] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:16,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c7b705f-48c3-464c-ac32-26966aadf5fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:16,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c7b705f-48c3-464c-ac32-26966aadf5fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:16,619] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:16,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:16,620] [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 endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	100.0	2521	2522	95	conclusive
Pseudonocardia sediminis	strain=DSM 45779	GCA_004217185.1	1397368	1397368	type	True	82.4543	1428	2522	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	81.2417	1274	2522	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	80.9542	1288	2522	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	80.7115	1306	2522	95	below_threshold
Pseudonocardia autotrophica	strain=NBRC 12743	GCA_003945385.1	2074	2074	suspected-type	True	80.6597	1313	2522	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_004361965.1	2074	2074	suspected-type	True	80.604	1333	2522	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	80.5905	1300	2522	95	below_threshold
Pseudonocardia terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	79.4858	1170	2522	95	below_threshold
Pseudonocardia pini	strain=CAP47R	GCA_013870575.1	2758030	2758030	type	True	79.4528	697	2522	95	below_threshold
Pseudonocardia bannensis	strain=DSM 45300	GCA_012911875.1	630973	630973	type	True	79.4178	936	2522	95	below_threshold
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	79.1368	1127	2522	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	79.0799	1246	2522	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	75.8568	837	2522	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:16,621] [INFO] DFAST Taxonomy check result was written to GCF_004339565.1_ASM433956v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:16,622] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:16,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:16,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c7b705f-48c3-464c-ac32-26966aadf5fa/dqc_reference/checkm_data
[2024-01-24 10:58:16,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:16,693] [INFO] Task started: CheckM
[2024-01-24 10:58:16,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339565.1_ASM433956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339565.1_ASM433956v1_genomic.fna/checkm_input GCF_004339565.1_ASM433956v1_genomic.fna/checkm_result
[2024-01-24 11:00:12,702] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:12,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.14%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:12,728] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:12,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:12,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339565.1_ASM433956v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:12,729] [INFO] Task started: Blastn
[2024-01-24 11:00:12,729] [INFO] Running command: blastn -query GCF_004339565.1_ASM433956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c7b705f-48c3-464c-ac32-26966aadf5fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339565.1_ASM433956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:14,721] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:14,724] [INFO] Selected 15 target genomes.
[2024-01-24 11:00:14,724] [INFO] Target genome list was writen to GCF_004339565.1_ASM433956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:14,734] [INFO] Task started: fastANI
[2024-01-24 11:00:14,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg37f2d6b4-4228-4cd7-818b-69ea462f698a/GCF_004339565.1_ASM433956v1_genomic.fna.gz --refList GCF_004339565.1_ASM433956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339565.1_ASM433956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:40,514] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:40,526] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:40,527] [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_004339565.1	s__Pseudonocardia endophytica	100.0	2521	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019263595.1	s__Pseudonocardia sp019263595	82.5458	1202	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217185.1	s__Pseudonocardia sediminis	82.4284	1433	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420995.1	s__Pseudonocardia sp001420995	81.3746	1341	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.03	98.66	0.91	0.86	8	-
GCA_002813375.1	s__Pseudonocardia alni	81.235	1276	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.52	96.72	0.89	0.85	6	-
GCF_014267175.1	s__Pseudonocardia sp014267175	81.0921	1187	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294645.1	s__Pseudonocardia sp001294645	81.0196	1217	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	96.56	96.19	0.82	0.80	7	-
GCF_900115005.1	s__Pseudonocardia ammonioxydans	80.9649	1285	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698125.1	s__Pseudonocardia sp001698125	80.7427	1211	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876315.1	s__Pseudonocardia parietis	80.7355	1303	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003945385.1	s__Pseudonocardia autotrophica	80.687	1309	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	100.00	100.00	1.00	1.00	4	-
GCF_012911875.1	s__Pseudonocardia bannensis	79.4201	936	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235185.1	s__Pseudonocardia sp014235185	79.1435	1127	2522	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	79.1027	1242	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695005.1	s__Pseudonocardia sp013695005	78.4439	351	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:40,528] [INFO] GTDB search result was written to GCF_004339565.1_ASM433956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:40,529] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:40,532] [INFO] DFAST_QC result json was written to GCF_004339565.1_ASM433956v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:40,532] [INFO] DFAST_QC completed!
[2024-01-24 11:00:40,532] [INFO] Total running time: 0h3m14s