[2024-01-24 14:19:01,497] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:01,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:01,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ff84fed-6275-4df7-a46f-f61d46a33b49/dqc_reference
[2024-01-24 14:19:02,931] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,932] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ac5bc95-c587-4711-938f-f7051711dc4d/GCF_007753265.1_ASM775326v1_genomic.fna.gz | prodigal -d GCF_007753265.1_ASM775326v1_genomic.fna/cds.fna -a GCF_007753265.1_ASM775326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:20,635] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:20,635] [INFO] Task started: HMMsearch
[2024-01-24 14:19:20,636] [INFO] Running command: hmmsearch --tblout GCF_007753265.1_ASM775326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ff84fed-6275-4df7-a46f-f61d46a33b49/dqc_reference/reference_markers.hmm GCF_007753265.1_ASM775326v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:20,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:20,954] [INFO] Found 6/6 markers.
[2024-01-24 14:19:21,005] [INFO] Query marker FASTA was written to GCF_007753265.1_ASM775326v1_genomic.fna/markers.fasta
[2024-01-24 14:19:21,006] [INFO] Task started: Blastn
[2024-01-24 14:19:21,006] [INFO] Running command: blastn -query GCF_007753265.1_ASM775326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ff84fed-6275-4df7-a46f-f61d46a33b49/dqc_reference/reference_markers.fasta -out GCF_007753265.1_ASM775326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:21,653] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:21,657] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:21,657] [INFO] Target genome list was writen to GCF_007753265.1_ASM775326v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:21,678] [INFO] Task started: fastANI
[2024-01-24 14:19:21,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac5bc95-c587-4711-938f-f7051711dc4d/GCF_007753265.1_ASM775326v1_genomic.fna.gz --refList GCF_007753265.1_ASM775326v1_genomic.fna/target_genomes.txt --output GCF_007753265.1_ASM775326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:37,228] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:37,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ff84fed-6275-4df7-a46f-f61d46a33b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:37,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ff84fed-6275-4df7-a46f-f61d46a33b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:37,238] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:37,239] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:37,239] [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
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	100.0	1957	1957	95	conclusive
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	81.1281	1034	1957	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	78.2342	546	1957	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	77.8753	337	1957	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	77.7979	502	1957	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	77.6343	507	1957	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	76.9028	290	1957	95	below_threshold
Aeromicrobium camelliae	strain=YS17T	GCA_003850045.1	1538144	1538144	type	True	74.8257	53	1957	95	below_threshold
Thermasporomyces composti	strain=DSM 22891	GCA_003386795.1	696763	696763	type	True	74.7641	57	1957	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	74.7194	179	1957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:37,240] [INFO] DFAST Taxonomy check result was written to GCF_007753265.1_ASM775326v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:37,241] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:37,241] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:37,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ff84fed-6275-4df7-a46f-f61d46a33b49/dqc_reference/checkm_data
[2024-01-24 14:19:37,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:37,306] [INFO] Task started: CheckM
[2024-01-24 14:19:37,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007753265.1_ASM775326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007753265.1_ASM775326v1_genomic.fna/checkm_input GCF_007753265.1_ASM775326v1_genomic.fna/checkm_result
[2024-01-24 14:20:30,283] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:30,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:30,300] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:30,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:30,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007753265.1_ASM775326v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:30,301] [INFO] Task started: Blastn
[2024-01-24 14:20:30,301] [INFO] Running command: blastn -query GCF_007753265.1_ASM775326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ff84fed-6275-4df7-a46f-f61d46a33b49/dqc_reference/reference_markers_gtdb.fasta -out GCF_007753265.1_ASM775326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:31,257] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:31,259] [INFO] Selected 11 target genomes.
[2024-01-24 14:20:31,259] [INFO] Target genome list was writen to GCF_007753265.1_ASM775326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:31,284] [INFO] Task started: fastANI
[2024-01-24 14:20:31,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac5bc95-c587-4711-938f-f7051711dc4d/GCF_007753265.1_ASM775326v1_genomic.fna.gz --refList GCF_007753265.1_ASM775326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007753265.1_ASM775326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:43,932] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:43,946] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:43,947] [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_007753265.1	s__Botrimarina mediterranea	100.0	1957	1957	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	conclusive
GCF_007859955.1	s__Botrimarina colliarenosi	81.1143	1034	1957	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	79.6491	751	1957	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859945.1	s__Pseudobythopirellula maris	78.2347	546	1957	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859815.1	s__Botrimarina hoheduenensis	77.8756	337	1957	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	77.7893	504	1957	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	77.638	507	1957	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822725.1	s__Lacipirellula sp013822725	76.8606	217	1957	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266075.1	s__SZAS-1 sp018266075	74.9504	107	1957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__SZAS-1;g__SZAS-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386795.1	s__Thermasporomyces composti	74.7641	57	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Thermasporomyces	95.0	99.77	99.77	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:43,948] [INFO] GTDB search result was written to GCF_007753265.1_ASM775326v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:43,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:43,952] [INFO] DFAST_QC result json was written to GCF_007753265.1_ASM775326v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:43,953] [INFO] DFAST_QC completed!
[2024-01-24 14:20:43,953] [INFO] Total running time: 0h1m42s