[2024-01-24 13:28:44,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ce983f5-429f-40b2-b9e9-da452d139b83/dqc_reference
[2024-01-24 13:28:45,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,847] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg54a785d7-f5b4-4e3f-8c8d-736636c92b94/GCF_007859855.1_ASM785985v1_genomic.fna.gz | prodigal -d GCF_007859855.1_ASM785985v1_genomic.fna/cds.fna -a GCF_007859855.1_ASM785985v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:29:11,064] [INFO] Task succeeded: Prodigal
[2024-01-24 13:29:11,065] [INFO] Task started: HMMsearch
[2024-01-24 13:29:11,065] [INFO] Running command: hmmsearch --tblout GCF_007859855.1_ASM785985v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ce983f5-429f-40b2-b9e9-da452d139b83/dqc_reference/reference_markers.hmm GCF_007859855.1_ASM785985v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:29:11,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:29:11,467] [INFO] Found 6/6 markers.
[2024-01-24 13:29:11,529] [INFO] Query marker FASTA was written to GCF_007859855.1_ASM785985v1_genomic.fna/markers.fasta
[2024-01-24 13:29:11,529] [INFO] Task started: Blastn
[2024-01-24 13:29:11,530] [INFO] Running command: blastn -query GCF_007859855.1_ASM785985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ce983f5-429f-40b2-b9e9-da452d139b83/dqc_reference/reference_markers.fasta -out GCF_007859855.1_ASM785985v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:12,253] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:12,256] [INFO] Selected 17 target genomes.
[2024-01-24 13:29:12,257] [INFO] Target genome list was writen to GCF_007859855.1_ASM785985v1_genomic.fna/target_genomes.txt
[2024-01-24 13:29:12,267] [INFO] Task started: fastANI
[2024-01-24 13:29:12,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg54a785d7-f5b4-4e3f-8c8d-736636c92b94/GCF_007859855.1_ASM785985v1_genomic.fna.gz --refList GCF_007859855.1_ASM785985v1_genomic.fna/target_genomes.txt --output GCF_007859855.1_ASM785985v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:38,354] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:38,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ce983f5-429f-40b2-b9e9-da452d139b83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:38,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ce983f5-429f-40b2-b9e9-da452d139b83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:38,371] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:38,372] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:38,372] [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
Rhodopirellula solitaria	strain=CA85	GCA_007859855.1	2527987	2527987	type	True	100.0	2231	2234	95	conclusive
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	77.5565	368	2234	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.3054	385	2234	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	77.1573	336	2234	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	76.9671	264	2234	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	76.6707	212	2234	95	below_threshold
Rosistilla carotiformis	strain=Poly24	GCA_007753095.1	2528017	2528017	type	True	76.3662	105	2234	95	below_threshold
Novipirellula aureliae	strain=Q31b	GCA_007860185.1	2527966	2527966	type	True	76.2623	108	2234	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.1316	166	2234	95	below_threshold
Rosistilla ulvae	strain=EC9	GCA_007741475.1	1930277	1930277	type	True	76.1213	115	2234	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.3367	63	2234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:38,374] [INFO] DFAST Taxonomy check result was written to GCF_007859855.1_ASM785985v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:38,375] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:38,376] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:38,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ce983f5-429f-40b2-b9e9-da452d139b83/dqc_reference/checkm_data
[2024-01-24 13:29:38,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:38,452] [INFO] Task started: CheckM
[2024-01-24 13:29:38,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007859855.1_ASM785985v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007859855.1_ASM785985v1_genomic.fna/checkm_input GCF_007859855.1_ASM785985v1_genomic.fna/checkm_result
[2024-01-24 13:30:50,033] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:50,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:50,057] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:50,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:50,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007859855.1_ASM785985v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:50,058] [INFO] Task started: Blastn
[2024-01-24 13:30:50,059] [INFO] Running command: blastn -query GCF_007859855.1_ASM785985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ce983f5-429f-40b2-b9e9-da452d139b83/dqc_reference/reference_markers_gtdb.fasta -out GCF_007859855.1_ASM785985v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:50,841] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:50,845] [INFO] Selected 15 target genomes.
[2024-01-24 13:30:50,845] [INFO] Target genome list was writen to GCF_007859855.1_ASM785985v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:50,858] [INFO] Task started: fastANI
[2024-01-24 13:30:50,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg54a785d7-f5b4-4e3f-8c8d-736636c92b94/GCF_007859855.1_ASM785985v1_genomic.fna.gz --refList GCF_007859855.1_ASM785985v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007859855.1_ASM785985v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:13,682] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:13,701] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:13,701] [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_007859855.1	s__Rhodopirellula solitaria	100.0	2232	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007860105.1	s__Rhodopirellula sp007860105	78.8891	714	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192335.1	s__Rhodopirellula rubra	77.5652	367	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_000346505.1	s__Rhodopirellula sallentina	77.165	334	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859915.1	s__Rhodopirellula pilleata	76.972	263	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007859835.1	s__Novipirellula sp007859835	76.9661	106	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	76.7177	209	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	76.6511	214	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860125.1	s__Rubripirellula tenax	76.362	169	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753095.1	s__Rosistilla carotiformis	76.3495	106	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	76.1819	167	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741475.1	s__Rosistilla sp007741475	76.107	116	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	75.3525	62	2234	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:13,703] [INFO] GTDB search result was written to GCF_007859855.1_ASM785985v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:13,704] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:13,709] [INFO] DFAST_QC result json was written to GCF_007859855.1_ASM785985v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:13,709] [INFO] DFAST_QC completed!
[2024-01-24 13:31:13,709] [INFO] Total running time: 0h2m29s