[2024-01-25 19:48:20,796] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:20,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:20,798] [INFO] DQC Reference Directory: /var/lib/cwl/stga4c0bcbd-6072-4b99-8d71-72438ee6a0de/dqc_reference
[2024-01-25 19:48:21,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:21,945] [INFO] Task started: Prodigal
[2024-01-25 19:48:21,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg5612a3ee-bfce-4740-9fe4-9431136b4b4e/GCF_030813915.1_ASM3081391v1_genomic.fna.gz | prodigal -d GCF_030813915.1_ASM3081391v1_genomic.fna/cds.fna -a GCF_030813915.1_ASM3081391v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:38,279] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:38,279] [INFO] Task started: HMMsearch
[2024-01-25 19:48:38,279] [INFO] Running command: hmmsearch --tblout GCF_030813915.1_ASM3081391v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4c0bcbd-6072-4b99-8d71-72438ee6a0de/dqc_reference/reference_markers.hmm GCF_030813915.1_ASM3081391v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:38,588] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:38,589] [INFO] Found 6/6 markers.
[2024-01-25 19:48:38,643] [INFO] Query marker FASTA was written to GCF_030813915.1_ASM3081391v1_genomic.fna/markers.fasta
[2024-01-25 19:48:38,643] [INFO] Task started: Blastn
[2024-01-25 19:48:38,643] [INFO] Running command: blastn -query GCF_030813915.1_ASM3081391v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c0bcbd-6072-4b99-8d71-72438ee6a0de/dqc_reference/reference_markers.fasta -out GCF_030813915.1_ASM3081391v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:39,796] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:39,798] [INFO] Selected 15 target genomes.
[2024-01-25 19:48:39,799] [INFO] Target genome list was writen to GCF_030813915.1_ASM3081391v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:39,800] [INFO] Task started: fastANI
[2024-01-25 19:48:39,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg5612a3ee-bfce-4740-9fe4-9431136b4b4e/GCF_030813915.1_ASM3081391v1_genomic.fna.gz --refList GCF_030813915.1_ASM3081391v1_genomic.fna/target_genomes.txt --output GCF_030813915.1_ASM3081391v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:03,949] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:03,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4c0bcbd-6072-4b99-8d71-72438ee6a0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:03,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4c0bcbd-6072-4b99-8d71-72438ee6a0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:03,965] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:49:03,965] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:49:03,965] [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
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	88.6465	1525	2256	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	88.4277	1257	2256	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	87.8988	1467	2256	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	85.4343	1123	2256	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	78.3354	726	2256	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	78.2429	718	2256	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	78.0609	713	2256	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	78.0184	669	2256	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.8935	663	2256	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.86	627	2256	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.8389	718	2256	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	77.6336	529	2256	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	77.4045	756	2256	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	77.2624	534	2256	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.2376	854	2256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:03,966] [INFO] DFAST Taxonomy check result was written to GCF_030813915.1_ASM3081391v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:03,967] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:03,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:03,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4c0bcbd-6072-4b99-8d71-72438ee6a0de/dqc_reference/checkm_data
[2024-01-25 19:49:03,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:04,035] [INFO] Task started: CheckM
[2024-01-25 19:49:04,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813915.1_ASM3081391v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813915.1_ASM3081391v1_genomic.fna/checkm_input GCF_030813915.1_ASM3081391v1_genomic.fna/checkm_result
[2024-01-25 19:50:11,100] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:11,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:11,120] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:11,120] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:11,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813915.1_ASM3081391v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:11,121] [INFO] Task started: Blastn
[2024-01-25 19:50:11,121] [INFO] Running command: blastn -query GCF_030813915.1_ASM3081391v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c0bcbd-6072-4b99-8d71-72438ee6a0de/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813915.1_ASM3081391v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:13,476] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:13,482] [INFO] Selected 6 target genomes.
[2024-01-25 19:50:13,482] [INFO] Target genome list was writen to GCF_030813915.1_ASM3081391v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:13,483] [INFO] Task started: fastANI
[2024-01-25 19:50:13,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg5612a3ee-bfce-4740-9fe4-9431136b4b4e/GCF_030813915.1_ASM3081391v1_genomic.fna.gz --refList GCF_030813915.1_ASM3081391v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813915.1_ASM3081391v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:25,622] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:25,628] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:50:25,628] [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_016653355.1	s__Rhodoplanes elegans	88.6392	1525	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCF_003258865.1	s__Rhodoplanes roseus	87.8867	1468	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377085.1	s__Rhodoplanes sp013377085	86.2191	1519	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009720755.1	s__Rhodoplanes serenus	85.1779	1378	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCF_000293785.1	s__Rhodoplanes sp000293785	82.9817	1071	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900218015.1	s__Rhodopseudomonas pentothenatexigens	78.3257	729	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:25,629] [INFO] GTDB search result was written to GCF_030813915.1_ASM3081391v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:25,630] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:25,635] [INFO] DFAST_QC result json was written to GCF_030813915.1_ASM3081391v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:25,635] [INFO] DFAST_QC completed!
[2024-01-25 19:50:25,635] [INFO] Total running time: 0h2m5s