[2024-01-25 20:04:20,594] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:20,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:20,596] [INFO] DQC Reference Directory: /var/lib/cwl/stgd42ab2a7-133d-45c4-abb9-9cd7527ec111/dqc_reference
[2024-01-25 20:04:21,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:21,836] [INFO] Task started: Prodigal
[2024-01-25 20:04:21,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg97f46e5e-10ce-4fa7-bf17-ec9c62e6d7f0/GCF_001620365.2_ASM162036v2_genomic.fna.gz | prodigal -d GCF_001620365.2_ASM162036v2_genomic.fna/cds.fna -a GCF_001620365.2_ASM162036v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:47,203] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:47,203] [INFO] Task started: HMMsearch
[2024-01-25 20:04:47,203] [INFO] Running command: hmmsearch --tblout GCF_001620365.2_ASM162036v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd42ab2a7-133d-45c4-abb9-9cd7527ec111/dqc_reference/reference_markers.hmm GCF_001620365.2_ASM162036v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:47,565] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:47,566] [INFO] Found 6/6 markers.
[2024-01-25 20:04:47,633] [INFO] Query marker FASTA was written to GCF_001620365.2_ASM162036v2_genomic.fna/markers.fasta
[2024-01-25 20:04:47,633] [INFO] Task started: Blastn
[2024-01-25 20:04:47,633] [INFO] Running command: blastn -query GCF_001620365.2_ASM162036v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd42ab2a7-133d-45c4-abb9-9cd7527ec111/dqc_reference/reference_markers.fasta -out GCF_001620365.2_ASM162036v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:48,826] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:48,828] [INFO] Selected 14 target genomes.
[2024-01-25 20:04:48,828] [INFO] Target genome list was writen to GCF_001620365.2_ASM162036v2_genomic.fna/target_genomes.txt
[2024-01-25 20:04:48,838] [INFO] Task started: fastANI
[2024-01-25 20:04:48,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg97f46e5e-10ce-4fa7-bf17-ec9c62e6d7f0/GCF_001620365.2_ASM162036v2_genomic.fna.gz --refList GCF_001620365.2_ASM162036v2_genomic.fna/target_genomes.txt --output GCF_001620365.2_ASM162036v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:23,410] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:23,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd42ab2a7-133d-45c4-abb9-9cd7527ec111/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:23,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd42ab2a7-133d-45c4-abb9-9cd7527ec111/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:23,420] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:05:23,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:23,420] [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 keratiniphila subsp. keratiniphila	strain=DSM 44409	GCA_001620365.2	227715	129921	type	True	100.0	2992	2996	95	conclusive
Amycolatopsis keratiniphila subsp. nogabecina	strain=FH 1893	GCA_001953855.1	208442	129921	type	True	98.8567	2757	2996	95	conclusive
Amycolatopsis japonica	strain=MG417-CF17	GCA_000732925.1	208439	208439	type	True	94.9668	2558	2996	95	below_threshold
Amycolatopsis roodepoortensis	strain=DSM 46661	GCA_014873915.1	700274	700274	type	True	92.5297	2459	2996	95	below_threshold
Amycolatopsis lurida	strain=DSM 43134	GCA_900105055.1	31959	31959	type	True	92.2029	2434	2996	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	91.1763	2383	2996	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	91.1168	2353	2996	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	90.9468	2177	2996	95	below_threshold
Amycolatopsis orientalis	strain=KCTC 9412	GCA_000478275.1	31958	31958	type	True	90.0603	2309	2996	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.6873	1652	2996	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.9573	1123	2996	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.1257	1027	2996	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.7036	1039	2996	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.1022	811	2996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:23,422] [INFO] DFAST Taxonomy check result was written to GCF_001620365.2_ASM162036v2_genomic.fna/tc_result.tsv
[2024-01-25 20:05:23,422] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:23,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:23,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd42ab2a7-133d-45c4-abb9-9cd7527ec111/dqc_reference/checkm_data
[2024-01-25 20:05:23,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:23,502] [INFO] Task started: CheckM
[2024-01-25 20:05:23,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001620365.2_ASM162036v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001620365.2_ASM162036v2_genomic.fna/checkm_input GCF_001620365.2_ASM162036v2_genomic.fna/checkm_result
[2024-01-25 20:07:08,658] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:08,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.82%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:08,680] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:08,681] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:08,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001620365.2_ASM162036v2_genomic.fna/markers.fasta)
[2024-01-25 20:07:08,682] [INFO] Task started: Blastn
[2024-01-25 20:07:08,682] [INFO] Running command: blastn -query GCF_001620365.2_ASM162036v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd42ab2a7-133d-45c4-abb9-9cd7527ec111/dqc_reference/reference_markers_gtdb.fasta -out GCF_001620365.2_ASM162036v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:10,618] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:10,620] [INFO] Selected 10 target genomes.
[2024-01-25 20:07:10,621] [INFO] Target genome list was writen to GCF_001620365.2_ASM162036v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:10,633] [INFO] Task started: fastANI
[2024-01-25 20:07:10,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg97f46e5e-10ce-4fa7-bf17-ec9c62e6d7f0/GCF_001620365.2_ASM162036v2_genomic.fna.gz --refList GCF_001620365.2_ASM162036v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001620365.2_ASM162036v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:37,499] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:37,506] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:37,506] [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_001620365.2	s__Amycolatopsis keratiniphila	100.0	2992	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.78	96.67	0.89	0.86	5	conclusive
GCF_000732925.1	s__Amycolatopsis japonica	94.9667	2558	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.30	96.67	0.90	0.88	4	-
GCF_014873915.1	s__Amycolatopsis roodepoortensis	92.5039	2463	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.45	96.45	0.88	0.88	2	-
GCF_000342005.1	s__Amycolatopsis decaplanina	92.4606	2307	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105055.1	s__Amycolatopsis lurida	92.2008	2434	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.56	95.13	0.93	0.86	3	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	91.2641	2406	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995215.1	s__Amycolatopsis azurea	91.192	2381	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002234405.1	s__Amycolatopsis thailandensis	90.9501	2176	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002849735.1	s__Amycolatopsis sp002849735	90.5435	2358	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000478275.1	s__Amycolatopsis orientalis	90.046	2312	2996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.64	96.64	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:37,507] [INFO] GTDB search result was written to GCF_001620365.2_ASM162036v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:37,508] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:37,511] [INFO] DFAST_QC result json was written to GCF_001620365.2_ASM162036v2_genomic.fna/dqc_result.json
[2024-01-25 20:07:37,511] [INFO] DFAST_QC completed!
[2024-01-25 20:07:37,511] [INFO] Total running time: 0h3m17s