[2024-01-25 19:47:51,149] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:51,158] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:51,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg26e4d6c6-6a08-47cd-aa0e-925b52527b13/dqc_reference
[2024-01-25 19:47:52,315] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:52,316] [INFO] Task started: Prodigal
[2024-01-25 19:47:52,316] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ceb18a1-bf49-4cbd-a6bf-224693c729ea/GCF_003385235.1_ASM338523v1_genomic.fna.gz | prodigal -d GCF_003385235.1_ASM338523v1_genomic.fna/cds.fna -a GCF_003385235.1_ASM338523v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:19,641] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:19,642] [INFO] Task started: HMMsearch
[2024-01-25 19:48:19,642] [INFO] Running command: hmmsearch --tblout GCF_003385235.1_ASM338523v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26e4d6c6-6a08-47cd-aa0e-925b52527b13/dqc_reference/reference_markers.hmm GCF_003385235.1_ASM338523v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:20,077] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:20,079] [INFO] Found 6/6 markers.
[2024-01-25 19:48:20,158] [INFO] Query marker FASTA was written to GCF_003385235.1_ASM338523v1_genomic.fna/markers.fasta
[2024-01-25 19:48:20,158] [INFO] Task started: Blastn
[2024-01-25 19:48:20,158] [INFO] Running command: blastn -query GCF_003385235.1_ASM338523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e4d6c6-6a08-47cd-aa0e-925b52527b13/dqc_reference/reference_markers.fasta -out GCF_003385235.1_ASM338523v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:21,463] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:21,469] [INFO] Selected 12 target genomes.
[2024-01-25 19:48:21,470] [INFO] Target genome list was writen to GCF_003385235.1_ASM338523v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:21,480] [INFO] Task started: fastANI
[2024-01-25 19:48:21,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ceb18a1-bf49-4cbd-a6bf-224693c729ea/GCF_003385235.1_ASM338523v1_genomic.fna.gz --refList GCF_003385235.1_ASM338523v1_genomic.fna/target_genomes.txt --output GCF_003385235.1_ASM338523v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:47,942] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:47,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26e4d6c6-6a08-47cd-aa0e-925b52527b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:47,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26e4d6c6-6a08-47cd-aa0e-925b52527b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:47,951] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:48:47,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:47,952] [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 circi	strain=DSM 45561	GCA_003385235.1	871959	871959	type	True	100.0	3086	3107	95	conclusive
Amycolatopsis dendrobii	strain=DR6-1	GCA_014145675.1	2760662	2760662	type	True	92.1931	2510	3107	95	below_threshold
Amycolatopsis nivea	strain=CFH S0261	GCA_004522235.1	1644109	1644109	type	True	92.1748	2478	3107	95	below_threshold
Amycolatopsis rubida	strain=DSM 44637	GCA_900115345.1	112413	112413	type	True	91.8969	2368	3107	95	below_threshold
Amycolatopsis benzoatilytica	strain=AK 16/65	GCA_000383915.1	346045	346045	type	True	86.6184	1953	3107	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	85.295	1776	3107	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.4849	1560	3107	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.8587	1094	3107	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.9907	897	3107	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	78.6933	676	3107	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.0642	772	3107	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	77.6829	738	3107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:47,953] [INFO] DFAST Taxonomy check result was written to GCF_003385235.1_ASM338523v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:47,953] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:47,953] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:47,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26e4d6c6-6a08-47cd-aa0e-925b52527b13/dqc_reference/checkm_data
[2024-01-25 19:48:47,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:48,040] [INFO] Task started: CheckM
[2024-01-25 19:48:48,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385235.1_ASM338523v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385235.1_ASM338523v1_genomic.fna/checkm_input GCF_003385235.1_ASM338523v1_genomic.fna/checkm_result
[2024-01-25 19:50:20,529] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:20,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:20,563] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:20,564] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:20,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385235.1_ASM338523v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:20,565] [INFO] Task started: Blastn
[2024-01-25 19:50:20,565] [INFO] Running command: blastn -query GCF_003385235.1_ASM338523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e4d6c6-6a08-47cd-aa0e-925b52527b13/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385235.1_ASM338523v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:22,526] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:22,528] [INFO] Selected 10 target genomes.
[2024-01-25 19:50:22,528] [INFO] Target genome list was writen to GCF_003385235.1_ASM338523v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:22,540] [INFO] Task started: fastANI
[2024-01-25 19:50:22,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ceb18a1-bf49-4cbd-a6bf-224693c729ea/GCF_003385235.1_ASM338523v1_genomic.fna.gz --refList GCF_003385235.1_ASM338523v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385235.1_ASM338523v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:47,659] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:47,666] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:47,666] [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_003385235.1	s__Amycolatopsis circi	100.0	3087	3107	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_014145675.1	s__Amycolatopsis sp014145675	92.2195	2506	3107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522235.1	s__Amycolatopsis nivea	92.1818	2477	3107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.97	97.28	0.91	0.88	6	-
GCF_002796545.1	s__Amycolatopsis sp002796545	91.9393	2357	3107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900115345.1	s__Amycolatopsis rubida	91.8626	2372	3107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.28	99.27	0.88	0.87	4	-
GCF_014174495.1	s__Amycolatopsis echigonensis	91.7589	2165	3107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	98.67	98.67	0.88	0.88	2	-
GCF_000411975.1	s__Amycolatopsis orientalis_D	91.4117	2251	3107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383915.1	s__Amycolatopsis benzoatilytica	86.6168	1953	3107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717335.1	s__Amycolatopsis jejuensis	85.2756	1780	3107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356825.1	s__Catenulispora rubra	76.1447	653	3107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:47,668] [INFO] GTDB search result was written to GCF_003385235.1_ASM338523v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:47,668] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:47,671] [INFO] DFAST_QC result json was written to GCF_003385235.1_ASM338523v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:47,671] [INFO] DFAST_QC completed!
[2024-01-25 19:50:47,671] [INFO] Total running time: 0h2m57s