[2023-06-19 04:59:06,816] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:59:06,820] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:59:06,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg57ba3f13-08dd-445d-a40c-712343424147/dqc_reference
[2023-06-19 04:59:08,290] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:59:08,290] [INFO] Task started: Prodigal
[2023-06-19 04:59:08,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg58bc3f18-81e9-4884-9bfe-13bdad911733/GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna.gz | prodigal -d GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/cds.fna -a GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:59:18,625] [INFO] Task succeeded: Prodigal
[2023-06-19 04:59:18,625] [INFO] Task started: HMMsearch
[2023-06-19 04:59:18,626] [INFO] Running command: hmmsearch --tblout GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57ba3f13-08dd-445d-a40c-712343424147/dqc_reference/reference_markers.hmm GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:59:18,877] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:59:18,878] [INFO] Found 6/6 markers.
[2023-06-19 04:59:18,919] [INFO] Query marker FASTA was written to GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/markers.fasta
[2023-06-19 04:59:18,920] [INFO] Task started: Blastn
[2023-06-19 04:59:18,920] [INFO] Running command: blastn -query GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57ba3f13-08dd-445d-a40c-712343424147/dqc_reference/reference_markers.fasta -out GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:19,804] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:19,811] [INFO] Selected 6 target genomes.
[2023-06-19 04:59:19,811] [INFO] Target genome list was writen to GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/target_genomes.txt
[2023-06-19 04:59:19,813] [INFO] Task started: fastANI
[2023-06-19 04:59:19,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg58bc3f18-81e9-4884-9bfe-13bdad911733/GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna.gz --refList GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/target_genomes.txt --output GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:59:25,701] [INFO] Task succeeded: fastANI
[2023-06-19 04:59:25,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57ba3f13-08dd-445d-a40c-712343424147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:59:25,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57ba3f13-08dd-445d-a40c-712343424147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:59:25,712] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2023-06-19 04:59:25,713] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 04:59:25,713] [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
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	95.4008	910	1107	95	conclusive
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	95.4008	910	1107	95	conclusive
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	94.1664	962	1107	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	94.1663	958	1107	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	80.5272	551	1107	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.5146	121	1107	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:59:25,715] [INFO] DFAST Taxonomy check result was written to GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/tc_result.tsv
[2023-06-19 04:59:25,715] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:59:25,716] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:59:25,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57ba3f13-08dd-445d-a40c-712343424147/dqc_reference/checkm_data
[2023-06-19 04:59:25,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:59:25,762] [INFO] Task started: CheckM
[2023-06-19 04:59:25,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/checkm_input GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/checkm_result
[2023-06-19 05:00:02,574] [INFO] Task succeeded: CheckM
[2023-06-19 05:00:02,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:00:02,606] [INFO] ===== Completeness check finished =====
[2023-06-19 05:00:02,606] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:00:02,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/markers.fasta)
[2023-06-19 05:00:02,607] [INFO] Task started: Blastn
[2023-06-19 05:00:02,607] [INFO] Running command: blastn -query GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57ba3f13-08dd-445d-a40c-712343424147/dqc_reference/reference_markers_gtdb.fasta -out GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:00:04,174] [INFO] Task succeeded: Blastn
[2023-06-19 05:00:04,180] [INFO] Selected 6 target genomes.
[2023-06-19 05:00:04,180] [INFO] Target genome list was writen to GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:00:04,184] [INFO] Task started: fastANI
[2023-06-19 05:00:04,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg58bc3f18-81e9-4884-9bfe-13bdad911733/GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna.gz --refList GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/target_genomes_gtdb.txt --output GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:00:09,643] [INFO] Task succeeded: fastANI
[2023-06-19 05:00:09,652] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:00:09,652] [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_001418225.1	s__Pannonibacter indicus	95.4008	910	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	96.01	95.55	0.94	0.89	12	conclusive
GCF_000382365.1	s__Pannonibacter phragmitetus	94.1664	962	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009915765.1	s__Pannonibacter sp009915765	80.7695	562	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_003012935.1	s__Pannonibacter carbonis	80.5302	550	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	79.1065	449	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	76.5303	121	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-19 05:00:09,656] [INFO] GTDB search result was written to GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:00:09,657] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:00:09,664] [INFO] DFAST_QC result json was written to GCA_937997675.1_R1_Bin_Bin_95_sub_1_genomic.fna/dqc_result.json
[2023-06-19 05:00:09,665] [INFO] DFAST_QC completed!
[2023-06-19 05:00:09,665] [INFO] Total running time: 0h1m3s