[2024-01-24 13:31:44,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg56052316-9cc9-44b8-91f6-36ef10d82a28/dqc_reference
[2024-01-24 13:31:45,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,678] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f2d3311-623f-4234-82c2-505cd5c6c35e/GCF_004923255.1_ASM492325v1_genomic.fna.gz | prodigal -d GCF_004923255.1_ASM492325v1_genomic.fna/cds.fna -a GCF_004923255.1_ASM492325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:57,772] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:57,773] [INFO] Task started: HMMsearch
[2024-01-24 13:31:57,773] [INFO] Running command: hmmsearch --tblout GCF_004923255.1_ASM492325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56052316-9cc9-44b8-91f6-36ef10d82a28/dqc_reference/reference_markers.hmm GCF_004923255.1_ASM492325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:58,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:58,108] [INFO] Found 6/6 markers.
[2024-01-24 13:31:58,190] [INFO] Query marker FASTA was written to GCF_004923255.1_ASM492325v1_genomic.fna/markers.fasta
[2024-01-24 13:31:58,190] [INFO] Task started: Blastn
[2024-01-24 13:31:58,190] [INFO] Running command: blastn -query GCF_004923255.1_ASM492325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56052316-9cc9-44b8-91f6-36ef10d82a28/dqc_reference/reference_markers.fasta -out GCF_004923255.1_ASM492325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:59,357] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:59,361] [INFO] Selected 12 target genomes.
[2024-01-24 13:31:59,362] [INFO] Target genome list was writen to GCF_004923255.1_ASM492325v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:59,367] [INFO] Task started: fastANI
[2024-01-24 13:31:59,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f2d3311-623f-4234-82c2-505cd5c6c35e/GCF_004923255.1_ASM492325v1_genomic.fna.gz --refList GCF_004923255.1_ASM492325v1_genomic.fna/target_genomes.txt --output GCF_004923255.1_ASM492325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:08,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:08,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56052316-9cc9-44b8-91f6-36ef10d82a28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:08,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56052316-9cc9-44b8-91f6-36ef10d82a28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:08,502] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:08,502] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:08,502] [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
Subtercola vilae	strain=DB165	GCA_004923255.1	2056433	2056433	type	True	100.0	1289	1293	95	conclusive
Subtercola lobariae	strain=CGMCC 1.12976	GCA_014640255.1	1588641	1588641	type	True	81.0899	574	1293	95	below_threshold
Subtercola lobariae	strain=9583b	GCA_016881145.1	1588641	1588641	type	True	81.0438	581	1293	95	below_threshold
Subtercola boreus	strain=K300	GCA_003399685.1	120213	120213	suspected-type	True	80.8694	629	1293	95	below_threshold
Subtercola boreus	strain=DSM 13056	GCA_006716115.1	120213	120213	suspected-type	True	80.8054	637	1293	95	below_threshold
Subtercola frigoramans	strain=DSM 13057	GCA_016907385.1	120298	120298	type	True	80.6507	529	1293	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.1662	443	1293	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.7644	444	1293	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.129	310	1293	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.1108	312	1293	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.1044	314	1293	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.9552	304	1293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:08,506] [INFO] DFAST Taxonomy check result was written to GCF_004923255.1_ASM492325v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:08,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:08,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:08,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56052316-9cc9-44b8-91f6-36ef10d82a28/dqc_reference/checkm_data
[2024-01-24 13:32:08,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:08,556] [INFO] Task started: CheckM
[2024-01-24 13:32:08,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004923255.1_ASM492325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004923255.1_ASM492325v1_genomic.fna/checkm_input GCF_004923255.1_ASM492325v1_genomic.fna/checkm_result
[2024-01-24 13:32:49,548] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:49,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:49,569] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:49,570] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:49,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004923255.1_ASM492325v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:49,571] [INFO] Task started: Blastn
[2024-01-24 13:32:49,571] [INFO] Running command: blastn -query GCF_004923255.1_ASM492325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56052316-9cc9-44b8-91f6-36ef10d82a28/dqc_reference/reference_markers_gtdb.fasta -out GCF_004923255.1_ASM492325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:51,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:51,234] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:51,235] [INFO] Target genome list was writen to GCF_004923255.1_ASM492325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:51,247] [INFO] Task started: fastANI
[2024-01-24 13:32:51,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f2d3311-623f-4234-82c2-505cd5c6c35e/GCF_004923255.1_ASM492325v1_genomic.fna.gz --refList GCF_004923255.1_ASM492325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004923255.1_ASM492325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:02,652] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:02,669] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:02,669] [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_004923255.1	s__Subtercola vilae	100.0	1289	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002931235.1	s__Subtercola sp002931235	81.5192	546	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640255.1	s__Subtercola lobariae	81.0979	573	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003399645.1	s__Subtercola boreus_A	80.8766	590	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	100.00	100.00	0.99	0.99	3	-
GCF_006716115.1	s__Subtercola boreus	80.8177	635	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003399625.1	s__Subtercola boreus_C	80.775	620	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399635.1	s__Subtercola boreus_B	80.7541	618	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018889995.1	s__Subtercola sp018889995	80.6871	516	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907385.1	s__Subtercola frigoramans	80.6698	527	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	75.6979	151	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000962825.1	s__Actinoplanes rectilineatus	75.2231	155	1293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:02,671] [INFO] GTDB search result was written to GCF_004923255.1_ASM492325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:02,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:02,677] [INFO] DFAST_QC result json was written to GCF_004923255.1_ASM492325v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:02,677] [INFO] DFAST_QC completed!
[2024-01-24 13:33:02,677] [INFO] Total running time: 0h1m18s