[2024-01-24 13:49:33,200] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg390b48de-8c56-41de-8936-4a979f73e61e/dqc_reference
[2024-01-24 13:49:34,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,595] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgee1079c6-e69f-44c6-a6bc-b920651e4b29/GCF_013407855.1_ASM1340785v1_genomic.fna.gz | prodigal -d GCF_013407855.1_ASM1340785v1_genomic.fna/cds.fna -a GCF_013407855.1_ASM1340785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:55,479] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:55,479] [INFO] Task started: HMMsearch
[2024-01-24 13:49:55,479] [INFO] Running command: hmmsearch --tblout GCF_013407855.1_ASM1340785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg390b48de-8c56-41de-8936-4a979f73e61e/dqc_reference/reference_markers.hmm GCF_013407855.1_ASM1340785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:55,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:55,918] [INFO] Found 6/6 markers.
[2024-01-24 13:49:55,972] [INFO] Query marker FASTA was written to GCF_013407855.1_ASM1340785v1_genomic.fna/markers.fasta
[2024-01-24 13:49:55,972] [INFO] Task started: Blastn
[2024-01-24 13:49:55,973] [INFO] Running command: blastn -query GCF_013407855.1_ASM1340785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg390b48de-8c56-41de-8936-4a979f73e61e/dqc_reference/reference_markers.fasta -out GCF_013407855.1_ASM1340785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:57,207] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:57,214] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:57,214] [INFO] Target genome list was writen to GCF_013407855.1_ASM1340785v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:57,219] [INFO] Task started: fastANI
[2024-01-24 13:49:57,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1079c6-e69f-44c6-a6bc-b920651e4b29/GCF_013407855.1_ASM1340785v1_genomic.fna.gz --refList GCF_013407855.1_ASM1340785v1_genomic.fna/target_genomes.txt --output GCF_013407855.1_ASM1340785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:19,182] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:19,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg390b48de-8c56-41de-8936-4a979f73e61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:19,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg390b48de-8c56-41de-8936-4a979f73e61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:19,195] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:19,196] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:19,196] [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 rutila	strain=DSM 18448	GCA_013407855.1	446787	446787	type	True	100.0	2315	2317	95	conclusive
Actinopolymorpha singaporensis	strain=DSM 22024	GCA_900104745.1	117157	117157	type	True	91.8056	1871	2317	95	below_threshold
Actinopolymorpha cephalotaxi	strain=DSM 45117	GCA_013408535.1	504797	504797	type	True	91.0975	1930	2317	95	below_threshold
Actinopolymorpha pittospori	strain=DSM 45354	GCA_014873875.1	648752	648752	type	True	81.3298	1403	2317	95	below_threshold
Actinopolymorpha alba	strain=DSM 45243	GCA_000373925.1	533267	533267	type	True	79.8609	1037	2317	95	below_threshold
Thermasporomyces composti	strain=DSM 22891	GCA_003386795.1	696763	696763	type	True	78.9144	705	2317	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.3704	514	2317	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.239	384	2317	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	77.2077	517	2317	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.8694	455	2317	95	below_threshold
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	76.8275	577	2317	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	76.7923	395	2317	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	76.5618	586	2317	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	76.3941	505	2317	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:19,198] [INFO] DFAST Taxonomy check result was written to GCF_013407855.1_ASM1340785v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:19,198] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:19,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:19,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg390b48de-8c56-41de-8936-4a979f73e61e/dqc_reference/checkm_data
[2024-01-24 13:50:19,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:19,271] [INFO] Task started: CheckM
[2024-01-24 13:50:19,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013407855.1_ASM1340785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013407855.1_ASM1340785v1_genomic.fna/checkm_input GCF_013407855.1_ASM1340785v1_genomic.fna/checkm_result
[2024-01-24 13:51:44,666] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:44,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:44,692] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:44,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:44,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013407855.1_ASM1340785v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:44,694] [INFO] Task started: Blastn
[2024-01-24 13:51:44,694] [INFO] Running command: blastn -query GCF_013407855.1_ASM1340785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg390b48de-8c56-41de-8936-4a979f73e61e/dqc_reference/reference_markers_gtdb.fasta -out GCF_013407855.1_ASM1340785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:46,573] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:46,577] [INFO] Selected 9 target genomes.
[2024-01-24 13:51:46,577] [INFO] Target genome list was writen to GCF_013407855.1_ASM1340785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:46,590] [INFO] Task started: fastANI
[2024-01-24 13:51:46,591] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1079c6-e69f-44c6-a6bc-b920651e4b29/GCF_013407855.1_ASM1340785v1_genomic.fna.gz --refList GCF_013407855.1_ASM1340785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013407855.1_ASM1340785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:00,685] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:00,697] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:00,697] [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_013407855.1	s__Actinopolymorpha rutila	100.0	2316	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900104745.1	s__Actinopolymorpha singaporensis	91.7943	1873	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408535.1	s__Actinopolymorpha cephalotaxi	91.1399	1924	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014873875.1	s__Actinopolymorpha pittospori	81.3109	1406	2317	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	79.8551	1039	2317	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	78.9717	698	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Thermasporomyces	95.0	99.77	99.77	0.94	0.94	2	-
GCF_000015265.1	s__Nocardioides sp000015265	77.1651	449	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013177455.1	s__Nocardioides sp013177455	76.9157	470	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_004349105.1	s__Jiangella aurantiaca	76.836	576	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:00,699] [INFO] GTDB search result was written to GCF_013407855.1_ASM1340785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:00,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:00,702] [INFO] DFAST_QC result json was written to GCF_013407855.1_ASM1340785v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:00,702] [INFO] DFAST_QC completed!
[2024-01-24 13:52:00,703] [INFO] Total running time: 0h2m28s