[2024-01-25 20:13:20,585] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:20,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:20,586] [INFO] DQC Reference Directory: /var/lib/cwl/stgefc32a96-d266-4bfa-ac62-9c87fab1988e/dqc_reference
[2024-01-25 20:13:21,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:21,692] [INFO] Task started: Prodigal
[2024-01-25 20:13:21,692] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf6c464f-261b-47a5-803b-7a631dad6ef0/GCF_014203365.1_ASM1420336v1_genomic.fna.gz | prodigal -d GCF_014203365.1_ASM1420336v1_genomic.fna/cds.fna -a GCF_014203365.1_ASM1420336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:41,340] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:41,340] [INFO] Task started: HMMsearch
[2024-01-25 20:13:41,340] [INFO] Running command: hmmsearch --tblout GCF_014203365.1_ASM1420336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefc32a96-d266-4bfa-ac62-9c87fab1988e/dqc_reference/reference_markers.hmm GCF_014203365.1_ASM1420336v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:41,602] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:41,603] [INFO] Found 6/6 markers.
[2024-01-25 20:13:41,650] [INFO] Query marker FASTA was written to GCF_014203365.1_ASM1420336v1_genomic.fna/markers.fasta
[2024-01-25 20:13:41,650] [INFO] Task started: Blastn
[2024-01-25 20:13:41,650] [INFO] Running command: blastn -query GCF_014203365.1_ASM1420336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefc32a96-d266-4bfa-ac62-9c87fab1988e/dqc_reference/reference_markers.fasta -out GCF_014203365.1_ASM1420336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:42,805] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:42,811] [INFO] Selected 6 target genomes.
[2024-01-25 20:13:42,811] [INFO] Target genome list was writen to GCF_014203365.1_ASM1420336v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:42,819] [INFO] Task started: fastANI
[2024-01-25 20:13:42,819] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf6c464f-261b-47a5-803b-7a631dad6ef0/GCF_014203365.1_ASM1420336v1_genomic.fna.gz --refList GCF_014203365.1_ASM1420336v1_genomic.fna/target_genomes.txt --output GCF_014203365.1_ASM1420336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:52,312] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:52,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefc32a96-d266-4bfa-ac62-9c87fab1988e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:52,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefc32a96-d266-4bfa-ac62-9c87fab1988e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:52,318] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:13:52,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:52,318] [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
Actinoalloteichus hymeniacidonis	strain=DSM 45092	GCA_014203365.1	340345	340345	type	True	100.0	2101	2102	95	conclusive
Actinoalloteichus hymeniacidonis	strain=HPA177(T) (=DSM 45092(T))	GCA_001747425.1	340345	340345	type	True	99.9995	2100	2102	95	conclusive
Actinoalloteichus fjordicus	strain=ADI127-7	GCA_001941625.1	1612552	1612552	type	True	82.1181	1359	2102	95	below_threshold
Actinoalloteichus hoggarensis	strain=DSM 45943	GCA_002234535.1	1470176	1470176	type	True	81.8263	1288	2102	95	below_threshold
Actinoalloteichus hoggarensis	strain=CECT 8639	GCA_014203625.1	1470176	1470176	type	True	81.8262	1266	2102	95	below_threshold
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	77.6455	632	2102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:52,319] [INFO] DFAST Taxonomy check result was written to GCF_014203365.1_ASM1420336v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:52,320] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:52,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:52,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefc32a96-d266-4bfa-ac62-9c87fab1988e/dqc_reference/checkm_data
[2024-01-25 20:13:52,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:52,379] [INFO] Task started: CheckM
[2024-01-25 20:13:52,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203365.1_ASM1420336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203365.1_ASM1420336v1_genomic.fna/checkm_input GCF_014203365.1_ASM1420336v1_genomic.fna/checkm_result
[2024-01-25 20:15:18,488] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:18,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:18,524] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:18,524] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:18,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203365.1_ASM1420336v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:18,528] [INFO] Task started: Blastn
[2024-01-25 20:15:18,528] [INFO] Running command: blastn -query GCF_014203365.1_ASM1420336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefc32a96-d266-4bfa-ac62-9c87fab1988e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203365.1_ASM1420336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:20,305] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:20,307] [INFO] Selected 13 target genomes.
[2024-01-25 20:15:20,307] [INFO] Target genome list was writen to GCF_014203365.1_ASM1420336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:20,335] [INFO] Task started: fastANI
[2024-01-25 20:15:20,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf6c464f-261b-47a5-803b-7a631dad6ef0/GCF_014203365.1_ASM1420336v1_genomic.fna.gz --refList GCF_014203365.1_ASM1420336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203365.1_ASM1420336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:38,535] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:38,544] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:38,544] [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_001747425.1	s__Actinoalloteichus hymeniacidonis	99.9995	2100	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001941625.1	s__Actinoalloteichus fjordicus	82.1701	1357	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.71	99.71	0.98	0.98	2	-
GCF_002234535.1	s__Actinoalloteichus hoggarensis	81.8165	1294	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000239155.1	s__Actinoalloteichus spitiensis	78.3408	505	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429185.1	s__Actinoalloteichus cyanogriseus	78.2889	566	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.50	99.47	0.98	0.97	3	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	77.7659	541	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204915.1	s__Crossiella cryophila	77.667	626	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405885.1	s__Gandjariella thermophila	77.5935	468	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	77.5651	581	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348985.1	s__Saccharopolyspora sp004348985	77.5069	596	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182415.1	s__Actinokineospora mzabensis	77.4441	603	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_900115565.1	s__Yuhushiella arida	77.2849	453	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016863395.1	s__Sphaerisporangium rufum	75.9503	391	2102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:38,545] [INFO] GTDB search result was written to GCF_014203365.1_ASM1420336v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:38,546] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:38,548] [INFO] DFAST_QC result json was written to GCF_014203365.1_ASM1420336v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:38,548] [INFO] DFAST_QC completed!
[2024-01-25 20:15:38,548] [INFO] Total running time: 0h2m18s