[2023-06-29 13:59:30,326] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:59:30,331] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:59:30,331] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1ba6f54-7110-419d-974c-f74480230f02/dqc_reference
[2023-06-29 13:59:31,622] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:59:31,623] [INFO] Task started: Prodigal
[2023-06-29 13:59:31,624] [INFO] Running command: gunzip -c /var/lib/cwl/stg6312952a-7e16-47c4-9788-8ee2fc25c466/GCA_021404525.1_ASM2140452v1_genomic.fna.gz | prodigal -d GCA_021404525.1_ASM2140452v1_genomic.fna/cds.fna -a GCA_021404525.1_ASM2140452v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:59:44,387] [INFO] Task succeeded: Prodigal
[2023-06-29 13:59:44,387] [INFO] Task started: HMMsearch
[2023-06-29 13:59:44,387] [INFO] Running command: hmmsearch --tblout GCA_021404525.1_ASM2140452v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1ba6f54-7110-419d-974c-f74480230f02/dqc_reference/reference_markers.hmm GCA_021404525.1_ASM2140452v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:59:44,671] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:59:44,673] [INFO] Found 6/6 markers.
[2023-06-29 13:59:44,719] [INFO] Query marker FASTA was written to GCA_021404525.1_ASM2140452v1_genomic.fna/markers.fasta
[2023-06-29 13:59:44,719] [INFO] Task started: Blastn
[2023-06-29 13:59:44,720] [INFO] Running command: blastn -query GCA_021404525.1_ASM2140452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1ba6f54-7110-419d-974c-f74480230f02/dqc_reference/reference_markers.fasta -out GCA_021404525.1_ASM2140452v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:59:45,464] [INFO] Task succeeded: Blastn
[2023-06-29 13:59:45,467] [INFO] Selected 30 target genomes.
[2023-06-29 13:59:45,468] [INFO] Target genome list was writen to GCA_021404525.1_ASM2140452v1_genomic.fna/target_genomes.txt
[2023-06-29 13:59:45,470] [INFO] Task started: fastANI
[2023-06-29 13:59:45,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg6312952a-7e16-47c4-9788-8ee2fc25c466/GCA_021404525.1_ASM2140452v1_genomic.fna.gz --refList GCA_021404525.1_ASM2140452v1_genomic.fna/target_genomes.txt --output GCA_021404525.1_ASM2140452v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:00:06,696] [INFO] Task succeeded: fastANI
[2023-06-29 14:00:06,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1ba6f54-7110-419d-974c-f74480230f02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:00:06,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1ba6f54-7110-419d-974c-f74480230f02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:00:06,709] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:00:06,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:00:06,710] [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
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	76.6521	89	1357	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	76.2402	126	1357	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	76.1219	90	1357	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	76.0566	90	1357	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.0387	80	1357	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	75.9555	83	1357	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:00:06,712] [INFO] DFAST Taxonomy check result was written to GCA_021404525.1_ASM2140452v1_genomic.fna/tc_result.tsv
[2023-06-29 14:00:06,712] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:00:06,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:00:06,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1ba6f54-7110-419d-974c-f74480230f02/dqc_reference/checkm_data
[2023-06-29 14:00:06,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:00:06,756] [INFO] Task started: CheckM
[2023-06-29 14:00:06,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021404525.1_ASM2140452v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021404525.1_ASM2140452v1_genomic.fna/checkm_input GCA_021404525.1_ASM2140452v1_genomic.fna/checkm_result
[2023-06-29 14:00:47,504] [INFO] Task succeeded: CheckM
[2023-06-29 14:00:47,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:00:47,526] [INFO] ===== Completeness check finished =====
[2023-06-29 14:00:47,527] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:00:47,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021404525.1_ASM2140452v1_genomic.fna/markers.fasta)
[2023-06-29 14:00:47,527] [INFO] Task started: Blastn
[2023-06-29 14:00:47,528] [INFO] Running command: blastn -query GCA_021404525.1_ASM2140452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1ba6f54-7110-419d-974c-f74480230f02/dqc_reference/reference_markers_gtdb.fasta -out GCA_021404525.1_ASM2140452v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:00:48,719] [INFO] Task succeeded: Blastn
[2023-06-29 14:00:48,723] [INFO] Selected 16 target genomes.
[2023-06-29 14:00:48,723] [INFO] Target genome list was writen to GCA_021404525.1_ASM2140452v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:00:48,761] [INFO] Task started: fastANI
[2023-06-29 14:00:48,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg6312952a-7e16-47c4-9788-8ee2fc25c466/GCA_021404525.1_ASM2140452v1_genomic.fna.gz --refList GCA_021404525.1_ASM2140452v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021404525.1_ASM2140452v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:00:58,500] [INFO] Task succeeded: fastANI
[2023-06-29 14:00:58,513] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:00:58,513] [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
GCA_000509225.1	s__Mf105b01 sp000509225	82.7302	983	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	98.75	98.75	0.94	0.94	2	-
GCA_003330885.1	s__Mf105b01 sp003330885	82.5651	947	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695905.1	s__Mf105b01 sp002695905	82.3598	816	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	99.79	99.79	0.82	0.82	2	-
GCA_002715765.1	s__Mf105b01 sp002715765	78.0234	200	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	99.04	98.86	0.91	0.89	5	-
GCA_002746275.1	s__Mf105b01 sp002746275	77.211	246	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	76.6539	89	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684405.1	s__Parvibaculum sp002684405	76.1662	92	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842875.1	s__Parvibaculum sp002842875	76.1262	71	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	76.1219	90	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	75.9501	90	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
--------------------------------------------------------------------------------
[2023-06-29 14:00:58,515] [INFO] GTDB search result was written to GCA_021404525.1_ASM2140452v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:00:58,516] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:00:58,519] [INFO] DFAST_QC result json was written to GCA_021404525.1_ASM2140452v1_genomic.fna/dqc_result.json
[2023-06-29 14:00:58,520] [INFO] DFAST_QC completed!
[2023-06-29 14:00:58,520] [INFO] Total running time: 0h1m28s