[2024-01-24 14:19:15,652] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,658] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd85318e-6f51-4cdc-9433-97061878e38c/dqc_reference
[2024-01-24 14:19:18,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,324] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bb208e8-0661-4c94-9e71-0e8b181a14f4/GCF_000974445.1_ASM97444v1_genomic.fna.gz | prodigal -d GCF_000974445.1_ASM97444v1_genomic.fna/cds.fna -a GCF_000974445.1_ASM97444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:15,302] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:15,303] [INFO] Task started: HMMsearch
[2024-01-24 14:20:15,303] [INFO] Running command: hmmsearch --tblout GCF_000974445.1_ASM97444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd85318e-6f51-4cdc-9433-97061878e38c/dqc_reference/reference_markers.hmm GCF_000974445.1_ASM97444v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:15,847] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:15,849] [INFO] Found 6/6 markers.
[2024-01-24 14:20:15,948] [INFO] Query marker FASTA was written to GCF_000974445.1_ASM97444v1_genomic.fna/markers.fasta
[2024-01-24 14:20:15,949] [INFO] Task started: Blastn
[2024-01-24 14:20:15,949] [INFO] Running command: blastn -query GCF_000974445.1_ASM97444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd85318e-6f51-4cdc-9433-97061878e38c/dqc_reference/reference_markers.fasta -out GCF_000974445.1_ASM97444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:17,604] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:17,609] [INFO] Selected 15 target genomes.
[2024-01-24 14:20:17,609] [INFO] Target genome list was writen to GCF_000974445.1_ASM97444v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:17,617] [INFO] Task started: fastANI
[2024-01-24 14:20:17,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bb208e8-0661-4c94-9e71-0e8b181a14f4/GCF_000974445.1_ASM97444v1_genomic.fna.gz --refList GCF_000974445.1_ASM97444v1_genomic.fna/target_genomes.txt --output GCF_000974445.1_ASM97444v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:21:01,339] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:01,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd85318e-6f51-4cdc-9433-97061878e38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:21:01,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd85318e-6f51-4cdc-9433-97061878e38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:21:01,356] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:21:01,357] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:21:01,357] [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
Lentzea aerocolonigenes	strain=NBRC 13195	GCA_000974445.1	68170	68170	type	True	100.0	3540	3541	95	conclusive
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	99.9873	3472	3541	95	conclusive
Lentzea aerocolonigenes	strain=NRRL B-3298	GCA_000719205.1	68170	68170	type	True	99.9724	3469	3541	95	conclusive
Lentzea alba	strain=NEAU-D13	GCA_011067745.1	2714351	2714351	type	True	89.1306	2452	3541	95	below_threshold
Lentzea kentuckyensis	strain=NRRL B-24416	GCA_002150765.1	360086	360086	type	True	89.1057	2375	3541	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	89.0142	2385	3541	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	88.8611	2313	3541	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	88.7849	2516	3541	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	88.0964	2226	3541	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	88.0046	2182	3541	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	87.8622	2239	3541	95	below_threshold
Lentzea albida	strain=DSM 44437	GCA_900111005.1	65499	65499	type	True	87.7934	2262	3541	95	below_threshold
Lentzea fradiae	strain=CGMCC 4.3506	GCA_900100955.1	200378	200378	type	True	86.7594	2027	3541	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.5424	1748	3541	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.117	1186	3541	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:21:01,359] [INFO] DFAST Taxonomy check result was written to GCF_000974445.1_ASM97444v1_genomic.fna/tc_result.tsv
[2024-01-24 14:21:01,359] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:21:01,359] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:21:01,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd85318e-6f51-4cdc-9433-97061878e38c/dqc_reference/checkm_data
[2024-01-24 14:21:01,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:21:01,484] [INFO] Task started: CheckM
[2024-01-24 14:21:01,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000974445.1_ASM97444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000974445.1_ASM97444v1_genomic.fna/checkm_input GCF_000974445.1_ASM97444v1_genomic.fna/checkm_result
[2024-01-24 14:24:48,211] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:48,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:48,238] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:48,238] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:48,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000974445.1_ASM97444v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:48,239] [INFO] Task started: Blastn
[2024-01-24 14:24:48,240] [INFO] Running command: blastn -query GCF_000974445.1_ASM97444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd85318e-6f51-4cdc-9433-97061878e38c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000974445.1_ASM97444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:53,077] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:53,081] [INFO] Selected 15 target genomes.
[2024-01-24 14:24:53,081] [INFO] Target genome list was writen to GCF_000974445.1_ASM97444v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:53,109] [INFO] Task started: fastANI
[2024-01-24 14:24:53,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bb208e8-0661-4c94-9e71-0e8b181a14f4/GCF_000974445.1_ASM97444v1_genomic.fna.gz --refList GCF_000974445.1_ASM97444v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000974445.1_ASM97444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:33,300] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:33,358] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:33,359] [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_000974445.1	s__Lentzea aerocolonigenes	100.0	3540	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_012184385.1	s__Lentzea indica	89.2747	2324	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150765.1	s__Lentzea kentuckyensis	89.1129	2373	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067745.1	s__Lentzea alba	89.0993	2459	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648475.1	s__Lentzea flava	89.0396	2364	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907955.1	s__Lentzea nigeriaca	88.8868	2433	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269295.1	s__Lentzea atacamensis	88.8525	2315	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	-
GCF_003265345.1	s__Lentzea terrae	88.7604	2520	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	88.1954	2198	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646255.1	s__Lentzea pudingi	87.9896	2185	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110955.1	s__Lentzea xinjiangensis	87.9641	2033	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653695.1	s__Lentzea cavernae	87.8978	2234	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111005.1	s__Lentzea albida	87.8275	2256	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104175.1	s__Lentzea jiangxiensis	87.7359	2061	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100955.1	s__Lentzea fradiae	86.7967	2022	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:33,360] [INFO] GTDB search result was written to GCF_000974445.1_ASM97444v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:33,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:33,365] [INFO] DFAST_QC result json was written to GCF_000974445.1_ASM97444v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:33,365] [INFO] DFAST_QC completed!
[2024-01-24 14:25:33,365] [INFO] Total running time: 0h6m18s