[2024-01-25 18:10:35,724] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:35,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:35,726] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1461878-9873-4341-ae87-4af7c456cd64/dqc_reference
[2024-01-25 18:10:36,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:36,892] [INFO] Task started: Prodigal
[2024-01-25 18:10:36,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg901f0c89-b297-43e3-acfb-7cf74df1d47c/GCF_001027925.1_K833_genomic.fna.gz | prodigal -d GCF_001027925.1_K833_genomic.fna/cds.fna -a GCF_001027925.1_K833_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:10,067] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:10,067] [INFO] Task started: HMMsearch
[2024-01-25 18:11:10,067] [INFO] Running command: hmmsearch --tblout GCF_001027925.1_K833_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1461878-9873-4341-ae87-4af7c456cd64/dqc_reference/reference_markers.hmm GCF_001027925.1_K833_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:10,385] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:10,386] [INFO] Found 6/6 markers.
[2024-01-25 18:11:10,443] [INFO] Query marker FASTA was written to GCF_001027925.1_K833_genomic.fna/markers.fasta
[2024-01-25 18:11:10,444] [INFO] Task started: Blastn
[2024-01-25 18:11:10,444] [INFO] Running command: blastn -query GCF_001027925.1_K833_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1461878-9873-4341-ae87-4af7c456cd64/dqc_reference/reference_markers.fasta -out GCF_001027925.1_K833_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:11,018] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:11,021] [INFO] Selected 13 target genomes.
[2024-01-25 18:11:11,021] [INFO] Target genome list was writen to GCF_001027925.1_K833_genomic.fna/target_genomes.txt
[2024-01-25 18:11:11,053] [INFO] Task started: fastANI
[2024-01-25 18:11:11,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg901f0c89-b297-43e3-acfb-7cf74df1d47c/GCF_001027925.1_K833_genomic.fna.gz --refList GCF_001027925.1_K833_genomic.fna/target_genomes.txt --output GCF_001027925.1_K833_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:31,396] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:31,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1461878-9873-4341-ae87-4af7c456cd64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:31,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1461878-9873-4341-ae87-4af7c456cd64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:31,403] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:11:31,403] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:31,403] [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 islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	100.0	2447	2448	95	conclusive
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	83.9473	1661	2448	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	83.577	1548	2448	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	83.2163	1590	2448	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	77.5076	298	2448	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	77.4554	277	2448	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.3859	291	2448	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	76.8828	304	2448	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	76.1689	167	2448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:31,404] [INFO] DFAST Taxonomy check result was written to GCF_001027925.1_K833_genomic.fna/tc_result.tsv
[2024-01-25 18:11:31,405] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:31,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:31,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1461878-9873-4341-ae87-4af7c456cd64/dqc_reference/checkm_data
[2024-01-25 18:11:31,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:31,474] [INFO] Task started: CheckM
[2024-01-25 18:11:31,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001027925.1_K833_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001027925.1_K833_genomic.fna/checkm_input GCF_001027925.1_K833_genomic.fna/checkm_result
[2024-01-25 18:14:47,782] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:47,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:47,801] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:47,801] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:47,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001027925.1_K833_genomic.fna/markers.fasta)
[2024-01-25 18:14:47,802] [INFO] Task started: Blastn
[2024-01-25 18:14:47,802] [INFO] Running command: blastn -query GCF_001027925.1_K833_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1461878-9873-4341-ae87-4af7c456cd64/dqc_reference/reference_markers_gtdb.fasta -out GCF_001027925.1_K833_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:48,638] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:48,640] [INFO] Selected 8 target genomes.
[2024-01-25 18:14:48,640] [INFO] Target genome list was writen to GCF_001027925.1_K833_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:48,656] [INFO] Task started: fastANI
[2024-01-25 18:14:48,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg901f0c89-b297-43e3-acfb-7cf74df1d47c/GCF_001027925.1_K833_genomic.fna.gz --refList GCF_001027925.1_K833_genomic.fna/target_genomes_gtdb.txt --output GCF_001027925.1_K833_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:07,650] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:07,656] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:07,657] [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_001027925.1	s__Rhodopirellula islandica	100.0	2447	2448	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002727185.1	s__Rhodopirellula bahusiensis	83.9448	1661	2448	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	83.5742	1549	2448	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCF_000196115.1	s__Rhodopirellula baltica	83.2154	1592	2448	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCF_000346505.1	s__Rhodopirellula sallentina	77.5056	299	2448	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	77.411	280	2448	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_007859915.1	s__Rhodopirellula pilleata	76.9211	306	2448	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741555.1	s__K23-9 sp007741555	76.8264	177	2448	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:07,658] [INFO] GTDB search result was written to GCF_001027925.1_K833_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:07,660] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:07,663] [INFO] DFAST_QC result json was written to GCF_001027925.1_K833_genomic.fna/dqc_result.json
[2024-01-25 18:15:07,663] [INFO] DFAST_QC completed!
[2024-01-25 18:15:07,663] [INFO] Total running time: 0h4m32s