[2024-01-24 13:58:42,493] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:42,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:42,495] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8071608-b6dc-4d46-824a-e22cf17c49bb/dqc_reference
[2024-01-24 13:58:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:43,882] [INFO] Task started: Prodigal
[2024-01-24 13:58:43,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg32c36e96-cf38-4a33-8a0c-61b712cdd7de/GCF_013408535.1_ASM1340853v1_genomic.fna.gz | prodigal -d GCF_013408535.1_ASM1340853v1_genomic.fna/cds.fna -a GCF_013408535.1_ASM1340853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:04,634] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:04,635] [INFO] Task started: HMMsearch
[2024-01-24 13:59:04,635] [INFO] Running command: hmmsearch --tblout GCF_013408535.1_ASM1340853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8071608-b6dc-4d46-824a-e22cf17c49bb/dqc_reference/reference_markers.hmm GCF_013408535.1_ASM1340853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:04,986] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:04,987] [INFO] Found 6/6 markers.
[2024-01-24 13:59:05,049] [INFO] Query marker FASTA was written to GCF_013408535.1_ASM1340853v1_genomic.fna/markers.fasta
[2024-01-24 13:59:05,050] [INFO] Task started: Blastn
[2024-01-24 13:59:05,050] [INFO] Running command: blastn -query GCF_013408535.1_ASM1340853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8071608-b6dc-4d46-824a-e22cf17c49bb/dqc_reference/reference_markers.fasta -out GCF_013408535.1_ASM1340853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:06,286] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:06,289] [INFO] Selected 12 target genomes.
[2024-01-24 13:59:06,290] [INFO] Target genome list was writen to GCF_013408535.1_ASM1340853v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:06,295] [INFO] Task started: fastANI
[2024-01-24 13:59:06,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c36e96-cf38-4a33-8a0c-61b712cdd7de/GCF_013408535.1_ASM1340853v1_genomic.fna.gz --refList GCF_013408535.1_ASM1340853v1_genomic.fna/target_genomes.txt --output GCF_013408535.1_ASM1340853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:24,845] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:24,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8071608-b6dc-4d46-824a-e22cf17c49bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:24,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8071608-b6dc-4d46-824a-e22cf17c49bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:24,863] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:24,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:24,863] [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
Actinopolymorpha cephalotaxi	strain=DSM 45117	GCA_013408535.1	504797	504797	type	True	100.0	2286	2286	95	conclusive
Actinopolymorpha rutila	strain=DSM 18448	GCA_013407855.1	446787	446787	type	True	91.1719	1924	2286	95	below_threshold
Actinopolymorpha singaporensis	strain=DSM 22024	GCA_900104745.1	117157	117157	type	True	90.5051	1839	2286	95	below_threshold
Actinopolymorpha pittospori	strain=DSM 45354	GCA_014873875.1	648752	648752	type	True	81.3251	1379	2286	95	below_threshold
Actinopolymorpha alba	strain=DSM 45243	GCA_000373925.1	533267	533267	type	True	79.8064	1048	2286	95	below_threshold
Thermasporomyces composti	strain=DSM 22891	GCA_003386795.1	696763	696763	type	True	78.9708	706	2286	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.6047	496	2286	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	77.1966	579	2286	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.1145	589	2286	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	77.0872	524	2286	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.997	454	2286	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	76.274	547	2286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:24,865] [INFO] DFAST Taxonomy check result was written to GCF_013408535.1_ASM1340853v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:24,866] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:24,866] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:24,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8071608-b6dc-4d46-824a-e22cf17c49bb/dqc_reference/checkm_data
[2024-01-24 13:59:24,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:24,935] [INFO] Task started: CheckM
[2024-01-24 13:59:24,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408535.1_ASM1340853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408535.1_ASM1340853v1_genomic.fna/checkm_input GCF_013408535.1_ASM1340853v1_genomic.fna/checkm_result
[2024-01-24 14:01:22,023] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:22,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:22,052] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:22,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:22,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408535.1_ASM1340853v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:22,053] [INFO] Task started: Blastn
[2024-01-24 14:01:22,053] [INFO] Running command: blastn -query GCF_013408535.1_ASM1340853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8071608-b6dc-4d46-824a-e22cf17c49bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408535.1_ASM1340853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:24,066] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:24,070] [INFO] Selected 7 target genomes.
[2024-01-24 14:01:24,070] [INFO] Target genome list was writen to GCF_013408535.1_ASM1340853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:24,084] [INFO] Task started: fastANI
[2024-01-24 14:01:24,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c36e96-cf38-4a33-8a0c-61b712cdd7de/GCF_013408535.1_ASM1340853v1_genomic.fna.gz --refList GCF_013408535.1_ASM1340853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408535.1_ASM1340853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:36,093] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:36,100] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:36,100] [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_013408535.1	s__Actinopolymorpha cephalotaxi	100.0	2285	2286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_013407855.1	s__Actinopolymorpha rutila	91.1911	1919	2286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104745.1	s__Actinopolymorpha singaporensis	90.504	1839	2286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873875.1	s__Actinopolymorpha pittospori	81.3136	1382	2286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373925.1	s__Actinopolymorpha alba	79.8112	1047	2286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386795.1	s__Thermasporomyces composti	78.9858	707	2286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Thermasporomyces	95.0	99.77	99.77	0.94	0.94	2	-
GCF_013177455.1	s__Nocardioides sp013177455	77.0738	499	2286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:36,102] [INFO] GTDB search result was written to GCF_013408535.1_ASM1340853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:36,102] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:36,105] [INFO] DFAST_QC result json was written to GCF_013408535.1_ASM1340853v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:36,105] [INFO] DFAST_QC completed!
[2024-01-24 14:01:36,105] [INFO] Total running time: 0h2m54s