[2024-01-24 12:46:49,291] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:49,292] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:49,292] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c5f849b-00a7-4626-9c63-0c16188d911a/dqc_reference
[2024-01-24 12:46:50,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:50,425] [INFO] Task started: Prodigal
[2024-01-24 12:46:50,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg87db2f2f-251d-45ac-ae99-18fdf318338a/GCF_000196115.1_ASM19611v1_genomic.fna.gz | prodigal -d GCF_000196115.1_ASM19611v1_genomic.fna/cds.fna -a GCF_000196115.1_ASM19611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:19,386] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:19,386] [INFO] Task started: HMMsearch
[2024-01-24 12:47:19,386] [INFO] Running command: hmmsearch --tblout GCF_000196115.1_ASM19611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c5f849b-00a7-4626-9c63-0c16188d911a/dqc_reference/reference_markers.hmm GCF_000196115.1_ASM19611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:19,686] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:19,687] [INFO] Found 6/6 markers.
[2024-01-24 12:47:19,737] [INFO] Query marker FASTA was written to GCF_000196115.1_ASM19611v1_genomic.fna/markers.fasta
[2024-01-24 12:47:19,737] [INFO] Task started: Blastn
[2024-01-24 12:47:19,738] [INFO] Running command: blastn -query GCF_000196115.1_ASM19611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c5f849b-00a7-4626-9c63-0c16188d911a/dqc_reference/reference_markers.fasta -out GCF_000196115.1_ASM19611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:20,323] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:20,326] [INFO] Selected 15 target genomes.
[2024-01-24 12:47:20,326] [INFO] Target genome list was writen to GCF_000196115.1_ASM19611v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:20,332] [INFO] Task started: fastANI
[2024-01-24 12:47:20,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg87db2f2f-251d-45ac-ae99-18fdf318338a/GCF_000196115.1_ASM19611v1_genomic.fna.gz --refList GCF_000196115.1_ASM19611v1_genomic.fna/target_genomes.txt --output GCF_000196115.1_ASM19611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:41,834] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:41,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c5f849b-00a7-4626-9c63-0c16188d911a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:41,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c5f849b-00a7-4626-9c63-0c16188d911a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:41,844] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:41,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:41,844] [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 baltica	strain=1	GCA_000196115.1	265606	265606	type	True	100.0	2381	2381	95	conclusive
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	88.8563	1867	2381	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	84.5383	1772	2381	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	83.1826	1586	2381	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	77.9458	320	2381	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.6986	277	2381	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	77.2521	288	2381	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	77.1997	303	2381	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.6033	208	2381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:41,847] [INFO] DFAST Taxonomy check result was written to GCF_000196115.1_ASM19611v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:41,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:41,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:41,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c5f849b-00a7-4626-9c63-0c16188d911a/dqc_reference/checkm_data
[2024-01-24 12:47:41,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:41,917] [INFO] Task started: CheckM
[2024-01-24 12:47:41,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000196115.1_ASM19611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000196115.1_ASM19611v1_genomic.fna/checkm_input GCF_000196115.1_ASM19611v1_genomic.fna/checkm_result
[2024-01-24 12:49:32,754] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:32,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:32,776] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:32,777] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:32,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000196115.1_ASM19611v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:32,777] [INFO] Task started: Blastn
[2024-01-24 12:49:32,777] [INFO] Running command: blastn -query GCF_000196115.1_ASM19611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c5f849b-00a7-4626-9c63-0c16188d911a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000196115.1_ASM19611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:33,540] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:33,543] [INFO] Selected 10 target genomes.
[2024-01-24 12:49:33,543] [INFO] Target genome list was writen to GCF_000196115.1_ASM19611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:33,550] [INFO] Task started: fastANI
[2024-01-24 12:49:33,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg87db2f2f-251d-45ac-ae99-18fdf318338a/GCF_000196115.1_ASM19611v1_genomic.fna.gz --refList GCF_000196115.1_ASM19611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000196115.1_ASM19611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:49,953] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:49,962] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:49,962] [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_000196115.1	s__Rhodopirellula baltica	100.0	2381	2381	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	conclusive
GCF_000338295.1	s__Rhodopirellula europaea	88.8667	1866	2381	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	84.5405	1773	2381	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027925.1	s__Rhodopirellula islandica	83.1817	1586	2381	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	77.9436	321	2381	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	77.252	288	2381	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	77.2151	306	2381	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	76.6499	176	2381	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	76.3133	228	2381	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:49,964] [INFO] GTDB search result was written to GCF_000196115.1_ASM19611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:49,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:49,967] [INFO] DFAST_QC result json was written to GCF_000196115.1_ASM19611v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:49,967] [INFO] DFAST_QC completed!
[2024-01-24 12:49:49,967] [INFO] Total running time: 0h3m1s