[2024-01-24 11:42:20,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,308] [INFO] DQC Reference Directory: /var/lib/cwl/stgf036dcee-1c19-4b8f-a553-d1efe8866772/dqc_reference
[2024-01-24 11:42:24,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b8fd4c6-021a-4b54-82c9-78f283585588/GCF_013410405.1_ASM1341040v1_genomic.fna.gz | prodigal -d GCF_013410405.1_ASM1341040v1_genomic.fna/cds.fna -a GCF_013410405.1_ASM1341040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:50,922] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:50,923] [INFO] Task started: HMMsearch
[2024-01-24 11:42:50,923] [INFO] Running command: hmmsearch --tblout GCF_013410405.1_ASM1341040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf036dcee-1c19-4b8f-a553-d1efe8866772/dqc_reference/reference_markers.hmm GCF_013410405.1_ASM1341040v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:51,261] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:51,263] [INFO] Found 6/6 markers.
[2024-01-24 11:42:51,322] [INFO] Query marker FASTA was written to GCF_013410405.1_ASM1341040v1_genomic.fna/markers.fasta
[2024-01-24 11:42:51,323] [INFO] Task started: Blastn
[2024-01-24 11:42:51,323] [INFO] Running command: blastn -query GCF_013410405.1_ASM1341040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf036dcee-1c19-4b8f-a553-d1efe8866772/dqc_reference/reference_markers.fasta -out GCF_013410405.1_ASM1341040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:52,662] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:52,666] [INFO] Selected 10 target genomes.
[2024-01-24 11:42:52,666] [INFO] Target genome list was writen to GCF_013410405.1_ASM1341040v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:52,922] [INFO] Task started: fastANI
[2024-01-24 11:42:52,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8fd4c6-021a-4b54-82c9-78f283585588/GCF_013410405.1_ASM1341040v1_genomic.fna.gz --refList GCF_013410405.1_ASM1341040v1_genomic.fna/target_genomes.txt --output GCF_013410405.1_ASM1341040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:11,191] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:11,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf036dcee-1c19-4b8f-a553-d1efe8866772/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:11,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf036dcee-1c19-4b8f-a553-d1efe8866772/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:11,208] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:11,209] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:11,209] [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 endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	100.0	2398	2398	95	conclusive
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	87.8906	1637	2398	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	87.7956	1792	2398	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	87.6575	1682	2398	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	87.6461	1685	2398	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	86.3297	1449	2398	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	81.8553	1336	2398	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.905	1090	2398	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	79.8492	1284	2398	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	79.1596	845	2398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:11,211] [INFO] DFAST Taxonomy check result was written to GCF_013410405.1_ASM1341040v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:11,212] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:11,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:11,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf036dcee-1c19-4b8f-a553-d1efe8866772/dqc_reference/checkm_data
[2024-01-24 11:43:11,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:11,284] [INFO] Task started: CheckM
[2024-01-24 11:43:11,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410405.1_ASM1341040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410405.1_ASM1341040v1_genomic.fna/checkm_input GCF_013410405.1_ASM1341040v1_genomic.fna/checkm_result
[2024-01-24 11:45:36,596] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:36,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:36,615] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:36,615] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:36,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410405.1_ASM1341040v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:36,616] [INFO] Task started: Blastn
[2024-01-24 11:45:36,616] [INFO] Running command: blastn -query GCF_013410405.1_ASM1341040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf036dcee-1c19-4b8f-a553-d1efe8866772/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410405.1_ASM1341040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:38,682] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:38,686] [INFO] Selected 9 target genomes.
[2024-01-24 11:45:38,687] [INFO] Target genome list was writen to GCF_013410405.1_ASM1341040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:38,694] [INFO] Task started: fastANI
[2024-01-24 11:45:38,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8fd4c6-021a-4b54-82c9-78f283585588/GCF_013410405.1_ASM1341040v1_genomic.fna.gz --refList GCF_013410405.1_ASM1341040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410405.1_ASM1341040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:56,206] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:56,221] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:56,221] [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_013410405.1	s__Amycolatopsis endophytica	100.0	2396	2398	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_003385215.1	s__Amycolatopsis thermalba	87.8758	1639	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.72	99.30	0.96	0.93	4	-
GCF_014653945.1	s__Amycolatopsis deserti	87.7908	1715	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000231075.2	s__Amycolatopsis sp000231075	87.7851	1775	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	-
GCF_000473265.1	s__Amycolatopsis thermoflava	87.7809	1794	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	98.72	98.72	0.92	0.92	2	-
GCF_000739085.1	s__Amycolatopsis methanolica	87.631	1687	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_011758745.1	s__Amycolatopsis granulosa	86.3103	1451	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_004522235.1	s__Amycolatopsis nivea	79.7936	1110	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.97	97.28	0.91	0.88	6	-
GCF_900115345.1	s__Amycolatopsis rubida	79.551	1102	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.28	99.27	0.88	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:56,223] [INFO] GTDB search result was written to GCF_013410405.1_ASM1341040v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:56,224] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:56,227] [INFO] DFAST_QC result json was written to GCF_013410405.1_ASM1341040v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:56,227] [INFO] DFAST_QC completed!
[2024-01-24 11:45:56,227] [INFO] Total running time: 0h3m36s