[2024-01-24 11:34:39,886] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:39,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:39,888] [INFO] DQC Reference Directory: /var/lib/cwl/stg189d3e3a-5cfa-4200-8904-ceae1c30bd1f/dqc_reference
[2024-01-24 11:34:41,194] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,195] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,195] [INFO] Running command: gunzip -c /var/lib/cwl/stgf25fa754-8dc5-458f-9ccb-17ab977f625f/GCF_018835585.1_ASM1883558v1_genomic.fna.gz | prodigal -d GCF_018835585.1_ASM1883558v1_genomic.fna/cds.fna -a GCF_018835585.1_ASM1883558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:53,321] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:53,321] [INFO] Task started: HMMsearch
[2024-01-24 11:34:53,321] [INFO] Running command: hmmsearch --tblout GCF_018835585.1_ASM1883558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg189d3e3a-5cfa-4200-8904-ceae1c30bd1f/dqc_reference/reference_markers.hmm GCF_018835585.1_ASM1883558v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:53,626] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:53,627] [INFO] Found 6/6 markers.
[2024-01-24 11:34:53,669] [INFO] Query marker FASTA was written to GCF_018835585.1_ASM1883558v1_genomic.fna/markers.fasta
[2024-01-24 11:34:53,669] [INFO] Task started: Blastn
[2024-01-24 11:34:53,669] [INFO] Running command: blastn -query GCF_018835585.1_ASM1883558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg189d3e3a-5cfa-4200-8904-ceae1c30bd1f/dqc_reference/reference_markers.fasta -out GCF_018835585.1_ASM1883558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:54,281] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:54,284] [INFO] Selected 21 target genomes.
[2024-01-24 11:34:54,285] [INFO] Target genome list was writen to GCF_018835585.1_ASM1883558v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:54,292] [INFO] Task started: fastANI
[2024-01-24 11:34:54,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgf25fa754-8dc5-458f-9ccb-17ab977f625f/GCF_018835585.1_ASM1883558v1_genomic.fna.gz --refList GCF_018835585.1_ASM1883558v1_genomic.fna/target_genomes.txt --output GCF_018835585.1_ASM1883558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:06,557] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:06,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg189d3e3a-5cfa-4200-8904-ceae1c30bd1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:06,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg189d3e3a-5cfa-4200-8904-ceae1c30bd1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:06,564] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:06,564] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:06,564] [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
Pelorhabdus rhamnosifermentans	strain=BoRhaA	GCA_018835585.1	2772457	2772457	type	True	100.0	1700	1703	95	conclusive
Sporomusa acidovorans	strain=DSM 3132	GCA_002257695.1	112900	112900	type	True	77.3791	85	1703	95	below_threshold
Sporomusa acidovorans	strain=Mol	GCA_900101845.1	112900	112900	type	True	77.2688	83	1703	95	below_threshold
Methylomusa anaerophila	strain=MMFC1	GCA_003966895.1	1930071	1930071	type	True	76.0777	51	1703	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:06,566] [INFO] DFAST Taxonomy check result was written to GCF_018835585.1_ASM1883558v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:06,566] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:06,567] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:06,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg189d3e3a-5cfa-4200-8904-ceae1c30bd1f/dqc_reference/checkm_data
[2024-01-24 11:35:06,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:06,617] [INFO] Task started: CheckM
[2024-01-24 11:35:06,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018835585.1_ASM1883558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018835585.1_ASM1883558v1_genomic.fna/checkm_input GCF_018835585.1_ASM1883558v1_genomic.fna/checkm_result
[2024-01-24 11:35:45,203] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:45,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:45,223] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:45,224] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:45,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018835585.1_ASM1883558v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:45,224] [INFO] Task started: Blastn
[2024-01-24 11:35:45,224] [INFO] Running command: blastn -query GCF_018835585.1_ASM1883558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg189d3e3a-5cfa-4200-8904-ceae1c30bd1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_018835585.1_ASM1883558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:46,039] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:46,043] [INFO] Selected 25 target genomes.
[2024-01-24 11:35:46,043] [INFO] Target genome list was writen to GCF_018835585.1_ASM1883558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:46,137] [INFO] Task started: fastANI
[2024-01-24 11:35:46,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgf25fa754-8dc5-458f-9ccb-17ab977f625f/GCF_018835585.1_ASM1883558v1_genomic.fna.gz --refList GCF_018835585.1_ASM1883558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018835585.1_ASM1883558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:01,021] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:01,029] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:01,030] [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_018835585.1	s__Pelorhabdus rhamnosifermentans	100.0	1700	1703	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__UMGS1260;f__UMGS1260;g__Pelorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000725345.1	s__Pelosinus sp000725345	77.7463	119	1703	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101845.1	s__Sporomusa acidovorans	77.2688	83	1703	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.98	99.98	0.98	0.98	2	-
GCA_017889705.1	s__Sporomusa sp017889705	76.6916	72	1703	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550105.1	s__UMGS1260 sp900550105	76.6343	118	1703	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__UMGS1260;f__UMGS1260;g__UMGS1260	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298735.1	s__CYSP01 sp001298735	76.4934	68	1703	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__CYSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889585.1	s__CTSoil-075 sp017889585	76.3558	62	1703	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__CTSoil-075	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966895.1	s__Methylomusa anaerophila	76.0264	50	1703	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Methylomusa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:01,031] [INFO] GTDB search result was written to GCF_018835585.1_ASM1883558v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:01,032] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:01,035] [INFO] DFAST_QC result json was written to GCF_018835585.1_ASM1883558v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:01,035] [INFO] DFAST_QC completed!
[2024-01-24 11:36:01,035] [INFO] Total running time: 0h1m21s