[2024-01-25 20:03:35,552] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:35,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:35,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg7076b8e6-2794-47f8-bd71-998ca2dcd84d/dqc_reference
[2024-01-25 20:03:36,729] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:36,730] [INFO] Task started: Prodigal
[2024-01-25 20:03:36,730] [INFO] Running command: gunzip -c /var/lib/cwl/stg811b93e7-2446-4819-981d-f85571323af9/GCF_028748065.1_ASM2874806v1_genomic.fna.gz | prodigal -d GCF_028748065.1_ASM2874806v1_genomic.fna/cds.fna -a GCF_028748065.1_ASM2874806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:45,490] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:45,491] [INFO] Task started: HMMsearch
[2024-01-25 20:03:45,491] [INFO] Running command: hmmsearch --tblout GCF_028748065.1_ASM2874806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7076b8e6-2794-47f8-bd71-998ca2dcd84d/dqc_reference/reference_markers.hmm GCF_028748065.1_ASM2874806v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:45,703] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:45,704] [INFO] Found 6/6 markers.
[2024-01-25 20:03:45,732] [INFO] Query marker FASTA was written to GCF_028748065.1_ASM2874806v1_genomic.fna/markers.fasta
[2024-01-25 20:03:45,732] [INFO] Task started: Blastn
[2024-01-25 20:03:45,732] [INFO] Running command: blastn -query GCF_028748065.1_ASM2874806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7076b8e6-2794-47f8-bd71-998ca2dcd84d/dqc_reference/reference_markers.fasta -out GCF_028748065.1_ASM2874806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:46,424] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:46,427] [INFO] Selected 28 target genomes.
[2024-01-25 20:03:46,427] [INFO] Target genome list was writen to GCF_028748065.1_ASM2874806v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:46,443] [INFO] Task started: fastANI
[2024-01-25 20:03:46,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg811b93e7-2446-4819-981d-f85571323af9/GCF_028748065.1_ASM2874806v1_genomic.fna.gz --refList GCF_028748065.1_ASM2874806v1_genomic.fna/target_genomes.txt --output GCF_028748065.1_ASM2874806v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:06,138] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:06,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7076b8e6-2794-47f8-bd71-998ca2dcd84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:06,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7076b8e6-2794-47f8-bd71-998ca2dcd84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:06,145] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:04:06,145] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:04:06,146] [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
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	79.0628	391	1157	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	76.6811	88	1157	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	76.6153	85	1157	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.5679	87	1157	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.5566	83	1157	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	76.5517	134	1157	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	76.4566	129	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:06,147] [INFO] DFAST Taxonomy check result was written to GCF_028748065.1_ASM2874806v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:06,147] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:06,148] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:06,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7076b8e6-2794-47f8-bd71-998ca2dcd84d/dqc_reference/checkm_data
[2024-01-25 20:04:06,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:06,202] [INFO] Task started: CheckM
[2024-01-25 20:04:06,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028748065.1_ASM2874806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028748065.1_ASM2874806v1_genomic.fna/checkm_input GCF_028748065.1_ASM2874806v1_genomic.fna/checkm_result
[2024-01-25 20:04:35,662] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:35,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:35,699] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:35,699] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:35,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028748065.1_ASM2874806v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:35,700] [INFO] Task started: Blastn
[2024-01-25 20:04:35,700] [INFO] Running command: blastn -query GCF_028748065.1_ASM2874806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7076b8e6-2794-47f8-bd71-998ca2dcd84d/dqc_reference/reference_markers_gtdb.fasta -out GCF_028748065.1_ASM2874806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:37,084] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:37,087] [INFO] Selected 15 target genomes.
[2024-01-25 20:04:37,087] [INFO] Target genome list was writen to GCF_028748065.1_ASM2874806v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:37,110] [INFO] Task started: fastANI
[2024-01-25 20:04:37,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg811b93e7-2446-4819-981d-f85571323af9/GCF_028748065.1_ASM2874806v1_genomic.fna.gz --refList GCF_028748065.1_ASM2874806v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028748065.1_ASM2874806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:47,010] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:47,018] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:04:47,018] [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_002388885.1	s__Marinicaulis sp002388885	79.319	483	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943565.1	s__Marinicaulis flavus	79.0626	391	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	78.1839	328	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002535.1	s__Marinicaulis sp013002535	77.0384	143	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	99.52	99.49	0.97	0.96	3	-
GCA_001767925.1	s__CV81 sp001767925	76.9381	100	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	76.9061	210	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640095.1	s__Aquisalinus flavus	76.5431	88	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	76.5356	135	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013151255.1	s__Marinicaulis sp013151255	76.3021	175	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125425.1	s__Amphiplicatus sp016125425	76.1753	125	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506635.1	s__CV81 sp003506635	76.0587	76	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:47,020] [INFO] GTDB search result was written to GCF_028748065.1_ASM2874806v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:47,020] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:47,023] [INFO] DFAST_QC result json was written to GCF_028748065.1_ASM2874806v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:47,024] [INFO] DFAST_QC completed!
[2024-01-25 20:04:47,024] [INFO] Total running time: 0h1m11s