[2024-01-24 13:32:56,680] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:56,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:56,682] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf0a16f5-da09-4b21-a56b-7089cb8d7829/dqc_reference
[2024-01-24 13:32:57,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:57,901] [INFO] Task started: Prodigal
[2024-01-24 13:32:57,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b6f34db-f0b2-4d4d-9b94-f0bea41b0374/GCF_003201285.1_ASM320128v1_genomic.fna.gz | prodigal -d GCF_003201285.1_ASM320128v1_genomic.fna/cds.fna -a GCF_003201285.1_ASM320128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:07,511] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:07,511] [INFO] Task started: HMMsearch
[2024-01-24 13:33:07,512] [INFO] Running command: hmmsearch --tblout GCF_003201285.1_ASM320128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf0a16f5-da09-4b21-a56b-7089cb8d7829/dqc_reference/reference_markers.hmm GCF_003201285.1_ASM320128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:07,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:07,819] [INFO] Found 6/6 markers.
[2024-01-24 13:33:07,860] [INFO] Query marker FASTA was written to GCF_003201285.1_ASM320128v1_genomic.fna/markers.fasta
[2024-01-24 13:33:07,861] [INFO] Task started: Blastn
[2024-01-24 13:33:07,861] [INFO] Running command: blastn -query GCF_003201285.1_ASM320128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf0a16f5-da09-4b21-a56b-7089cb8d7829/dqc_reference/reference_markers.fasta -out GCF_003201285.1_ASM320128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:08,513] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:08,517] [INFO] Selected 26 target genomes.
[2024-01-24 13:33:08,517] [INFO] Target genome list was writen to GCF_003201285.1_ASM320128v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:08,652] [INFO] Task started: fastANI
[2024-01-24 13:33:08,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b6f34db-f0b2-4d4d-9b94-f0bea41b0374/GCF_003201285.1_ASM320128v1_genomic.fna.gz --refList GCF_003201285.1_ASM320128v1_genomic.fna/target_genomes.txt --output GCF_003201285.1_ASM320128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:22,006] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:22,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf0a16f5-da09-4b21-a56b-7089cb8d7829/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:22,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf0a16f5-da09-4b21-a56b-7089cb8d7829/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:22,019] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:22,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:22,020] [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
Lachnotalea glycerini	strain=DSM 28816	GCA_003201285.1	1763509	1763509	type	True	100.0	1593	1594	95	conclusive
Konateibacter massiliensis	strain=Marseille-P3773	GCA_900184995.1	2002841	2002841	type	True	77.9836	285	1594	95	below_threshold
Anaerosacchariphilus polymeriproducens	strain=MCWD5	GCA_003363435.1	1812858	1812858	type	True	76.9972	106	1594	95	below_threshold
Velocimicrobium porci	strain=WCA-693-APC-MOT-I	GCA_009696045.1	2606634	2606634	type	True	76.894	65	1594	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	76.5967	94	1594	95	below_threshold
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	76.3957	70	1594	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	76.2121	75	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:22,021] [INFO] DFAST Taxonomy check result was written to GCF_003201285.1_ASM320128v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:22,021] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:22,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:22,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf0a16f5-da09-4b21-a56b-7089cb8d7829/dqc_reference/checkm_data
[2024-01-24 13:33:22,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:22,068] [INFO] Task started: CheckM
[2024-01-24 13:33:22,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201285.1_ASM320128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201285.1_ASM320128v1_genomic.fna/checkm_input GCF_003201285.1_ASM320128v1_genomic.fna/checkm_result
[2024-01-24 13:33:55,652] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:55,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:55,675] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:55,676] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:55,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201285.1_ASM320128v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:55,677] [INFO] Task started: Blastn
[2024-01-24 13:33:55,677] [INFO] Running command: blastn -query GCF_003201285.1_ASM320128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf0a16f5-da09-4b21-a56b-7089cb8d7829/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201285.1_ASM320128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:56,684] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:56,689] [INFO] Selected 21 target genomes.
[2024-01-24 13:33:56,689] [INFO] Target genome list was writen to GCF_003201285.1_ASM320128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:56,720] [INFO] Task started: fastANI
[2024-01-24 13:33:56,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b6f34db-f0b2-4d4d-9b94-f0bea41b0374/GCF_003201285.1_ASM320128v1_genomic.fna.gz --refList GCF_003201285.1_ASM320128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201285.1_ASM320128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:09,226] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:09,242] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:09,243] [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_003201285.1	s__Lachnotalea glycerini	100.0	1593	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnotalea	95.0	99.47	99.47	0.92	0.92	2	conclusive
GCF_008830185.1	s__Lachnotalea soehngenii	78.5854	412	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnotalea	95.0	98.91	98.91	0.90	0.90	2	-
GCA_900184995.1	s__Lachnotalea sp900184995	77.976	284	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918265.1	s__Falcatimonas sp018918265	77.2826	60	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCF_003363435.1	s__Anaerosacchariphilus polymeriproducens	76.9803	105	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosacchariphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540475.1	s__Robinsoniella sp900540475	76.9436	66	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Robinsoniella	95.0	99.99	99.99	0.98	0.98	2	-
GCF_001940245.1	s__Fimousia sp001940245	76.94	50	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fimousia	95.0	99.44	99.44	0.97	0.97	2	-
GCF_009696045.1	s__Velocimicrobium porci	76.894	65	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Velocimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016591975.1	s__TB5 sp016591975	76.8014	78	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TB5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752155.1	s__Mobilisporobacter senegalensis	76.5967	94	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070565.1	s__Anaerosporobacter sp012070565	76.3957	70	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940225.1	s__14-2 sp001940225	76.3644	90	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315735.1	s__RUG115 sp900315735	76.1882	55	1594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	99.35	98.93	0.92	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:09,245] [INFO] GTDB search result was written to GCF_003201285.1_ASM320128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:09,246] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:09,251] [INFO] DFAST_QC result json was written to GCF_003201285.1_ASM320128v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:09,251] [INFO] DFAST_QC completed!
[2024-01-24 13:34:09,251] [INFO] Total running time: 0h1m13s