[2024-01-24 13:28:01,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,792] [INFO] DQC Reference Directory: /var/lib/cwl/stga96cb544-7f34-4483-9be9-7ae05b041b80/dqc_reference
[2024-01-24 13:28:02,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:02,990] [INFO] Task started: Prodigal
[2024-01-24 13:28:02,990] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a3a181e-2a32-483b-97c3-f6a85362207a/GCF_007859815.1_ASM785981v1_genomic.fna.gz | prodigal -d GCF_007859815.1_ASM785981v1_genomic.fna/cds.fna -a GCF_007859815.1_ASM785981v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:16,610] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:16,611] [INFO] Task started: HMMsearch
[2024-01-24 13:28:16,611] [INFO] Running command: hmmsearch --tblout GCF_007859815.1_ASM785981v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga96cb544-7f34-4483-9be9-7ae05b041b80/dqc_reference/reference_markers.hmm GCF_007859815.1_ASM785981v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:16,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:16,876] [INFO] Found 6/6 markers.
[2024-01-24 13:28:16,911] [INFO] Query marker FASTA was written to GCF_007859815.1_ASM785981v1_genomic.fna/markers.fasta
[2024-01-24 13:28:16,912] [INFO] Task started: Blastn
[2024-01-24 13:28:16,912] [INFO] Running command: blastn -query GCF_007859815.1_ASM785981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga96cb544-7f34-4483-9be9-7ae05b041b80/dqc_reference/reference_markers.fasta -out GCF_007859815.1_ASM785981v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:17,556] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:17,559] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:17,559] [INFO] Target genome list was writen to GCF_007859815.1_ASM785981v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:17,582] [INFO] Task started: fastANI
[2024-01-24 13:28:17,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a3a181e-2a32-483b-97c3-f6a85362207a/GCF_007859815.1_ASM785981v1_genomic.fna.gz --refList GCF_007859815.1_ASM785981v1_genomic.fna/target_genomes.txt --output GCF_007859815.1_ASM785981v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:29,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:29,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga96cb544-7f34-4483-9be9-7ae05b041b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:29,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga96cb544-7f34-4483-9be9-7ae05b041b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:29,572] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:29,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:29,573] [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 hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	100.0	1431	1431	95	conclusive
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	78.9388	388	1431	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	78.2858	322	1431	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	78.0286	334	1431	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	77.5144	256	1431	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	77.3983	269	1431	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.8714	263	1431	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	75.4583	55	1431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:29,574] [INFO] DFAST Taxonomy check result was written to GCF_007859815.1_ASM785981v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:29,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:29,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:29,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga96cb544-7f34-4483-9be9-7ae05b041b80/dqc_reference/checkm_data
[2024-01-24 13:28:29,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:29,619] [INFO] Task started: CheckM
[2024-01-24 13:28:29,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007859815.1_ASM785981v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007859815.1_ASM785981v1_genomic.fna/checkm_input GCF_007859815.1_ASM785981v1_genomic.fna/checkm_result
[2024-01-24 13:29:09,273] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:09,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:09,291] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:09,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:09,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007859815.1_ASM785981v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:09,292] [INFO] Task started: Blastn
[2024-01-24 13:29:09,292] [INFO] Running command: blastn -query GCF_007859815.1_ASM785981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga96cb544-7f34-4483-9be9-7ae05b041b80/dqc_reference/reference_markers_gtdb.fasta -out GCF_007859815.1_ASM785981v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:10,119] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:10,122] [INFO] Selected 14 target genomes.
[2024-01-24 13:29:10,122] [INFO] Target genome list was writen to GCF_007859815.1_ASM785981v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:10,136] [INFO] Task started: fastANI
[2024-01-24 13:29:10,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a3a181e-2a32-483b-97c3-f6a85362207a/GCF_007859815.1_ASM785981v1_genomic.fna.gz --refList GCF_007859815.1_ASM785981v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007859815.1_ASM785981v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:21,861] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:21,871] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:21,871] [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_007859815.1	s__Botrimarina hoheduenensis	100.0	1431	1431	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859955.1	s__Botrimarina colliarenosi	78.9388	388	1431	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	78.298	321	1431	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753265.1	s__Botrimarina mediterranea	78.0393	333	1431	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCA_007745835.1	s__Botrimarina sp007745835	77.9299	355	1431	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	77.5144	256	1431	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	77.4092	268	1431	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007750855.1	s__Pirellulimonas nuda	76.8466	266	1431	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003389215.1	s__MB-PLM-2 sp003389215	76.3608	78	1431	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA7805;g__MB-PLM-2	95.0	99.69	99.49	0.94	0.93	4	-
GCA_903958265.1	s__QWPN01 sp903958265	76.2236	55	1431	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_003671185.1	s__QWPN01 sp003671185	75.9404	60	1431	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931995.1	s__JAFGDS01 sp016931995	75.6319	61	1431	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGDS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:21,873] [INFO] GTDB search result was written to GCF_007859815.1_ASM785981v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:21,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:21,877] [INFO] DFAST_QC result json was written to GCF_007859815.1_ASM785981v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:21,877] [INFO] DFAST_QC completed!
[2024-01-24 13:29:21,877] [INFO] Total running time: 0h1m20s