[2023-06-05 18:57:25,024] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:57:25,039] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:57:25,039] [INFO] DQC Reference Directory: /var/lib/cwl/stge494a7c5-76c7-4388-931e-07b2f66cadf9/dqc_reference
[2023-06-05 18:57:26,578] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:57:26,579] [INFO] Task started: Prodigal
[2023-06-05 18:57:26,579] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc735fdb-a252-426f-8b99-db865ddcfaf8/GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna.gz | prodigal -d GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/cds.fna -a GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:29,871] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:29,872] [INFO] Task started: HMMsearch
[2023-06-05 18:57:29,872] [INFO] Running command: hmmsearch --tblout GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge494a7c5-76c7-4388-931e-07b2f66cadf9/dqc_reference/reference_markers.hmm GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:30,189] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:30,191] [INFO] Found 6/6 markers.
[2023-06-05 18:57:30,231] [INFO] Query marker FASTA was written to GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/markers.fasta
[2023-06-05 18:57:30,231] [INFO] Task started: Blastn
[2023-06-05 18:57:30,231] [INFO] Running command: blastn -query GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/markers.fasta -db /var/lib/cwl/stge494a7c5-76c7-4388-931e-07b2f66cadf9/dqc_reference/reference_markers.fasta -out GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:30,851] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:30,856] [INFO] Selected 29 target genomes.
[2023-06-05 18:57:30,856] [INFO] Target genome list was writen to GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/target_genomes.txt
[2023-06-05 18:57:30,884] [INFO] Task started: fastANI
[2023-06-05 18:57:30,885] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc735fdb-a252-426f-8b99-db865ddcfaf8/GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna.gz --refList GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/target_genomes.txt --output GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:57:45,872] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:45,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge494a7c5-76c7-4388-931e-07b2f66cadf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:57:45,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge494a7c5-76c7-4388-931e-07b2f66cadf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:57:45,881] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:57:45,881] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:57:45,881] [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
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	77.3968	81	560	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	77.3274	83	560	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	76.9078	61	560	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	76.6797	58	560	95	below_threshold
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	76.4281	50	560	95	below_threshold
Acetitomaculum ruminis	strain=DSM 5522	GCA_900112085.1	2382	2382	type	True	76.0609	50	560	95	below_threshold
Velocimicrobium porci	strain=WCA-693-APC-MOT-I	GCA_009696045.1	2606634	2606634	type	True	76.0344	50	560	95	below_threshold
[Clostridium] fimetarium	strain=DSM 9179	GCA_900111235.1	99656	99656	type	True	75.5823	56	560	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	75.5388	51	560	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:57:45,884] [INFO] DFAST Taxonomy check result was written to GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/tc_result.tsv
[2023-06-05 18:57:45,884] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:57:45,885] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:57:45,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge494a7c5-76c7-4388-931e-07b2f66cadf9/dqc_reference/checkm_data
[2023-06-05 18:57:45,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:57:45,910] [INFO] Task started: CheckM
[2023-06-05 18:57:45,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/checkm_input GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/checkm_result
[2023-06-05 18:58:03,590] [INFO] Task succeeded: CheckM
[2023-06-05 18:58:03,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:58:03,626] [INFO] ===== Completeness check finished =====
[2023-06-05 18:58:03,626] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:58:03,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/markers.fasta)
[2023-06-05 18:58:03,627] [INFO] Task started: Blastn
[2023-06-05 18:58:03,627] [INFO] Running command: blastn -query GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/markers.fasta -db /var/lib/cwl/stge494a7c5-76c7-4388-931e-07b2f66cadf9/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:04,437] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:04,443] [INFO] Selected 22 target genomes.
[2023-06-05 18:58:04,444] [INFO] Target genome list was writen to GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:58:04,480] [INFO] Task started: fastANI
[2023-06-05 18:58:04,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc735fdb-a252-426f-8b99-db865ddcfaf8/GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna.gz --refList GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/target_genomes_gtdb.txt --output GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:58:15,281] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:15,301] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:58:15,302] [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_900110975.1	s__CAG-603 sp900110975	98.3874	535	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.39	98.39	0.96	0.96	2	conclusive
GCA_902362455.1	s__CAG-603 sp900066105	77.9826	121	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.95	98.18	0.94	0.88	5	-
GCA_900314555.1	s__CAG-603 sp900314555	77.7434	129	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900315425.1	s__CAG-603 sp900315425	77.7235	140	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.93	98.30	0.88	0.81	6	-
GCA_017416465.1	s__CAG-603 sp017416465	77.5293	130	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016282745.1	s__SIG293 sp016282745	77.4629	78	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG293	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314525.1	s__CAG-603 sp900314525	77.4501	127	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.63	99.55	0.90	0.85	5	-
GCA_905215405.1	s__Clostridium_N sp905215405	77.4157	60	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_N	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057425.1	s__CAG-303 sp015057425	77.2462	67	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918265.1	s__Falcatimonas sp018918265	77.2118	68	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_017396555.1	s__RGIG1934 sp017396555	77.1892	79	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG1934	95.0	98.25	98.25	0.84	0.84	2	-
GCA_902363805.1	s__Eubacterium_G sp000434315	76.9629	89	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
GCA_902763335.1	s__UBA2821 sp902763335	76.9527	91	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539455.1	s__CAG-303 sp900539455	76.8534	65	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	99.77	99.53	0.98	0.96	3	-
GCA_902773095.1	s__CAG-603 sp902773095	76.7491	77	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.47	99.47	0.82	0.82	2	-
GCA_902786365.1	s__CAG-603 sp902786365	76.6111	99	560	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:58:15,304] [INFO] GTDB search result was written to GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/result_gtdb.tsv
[2023-06-05 18:58:15,305] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:58:15,311] [INFO] DFAST_QC result json was written to GCA_902782775.1_Rumen_uncultured_genome_RUG12796_genomic.fna/dqc_result.json
[2023-06-05 18:58:15,311] [INFO] DFAST_QC completed!
[2023-06-05 18:58:15,312] [INFO] Total running time: 0h0m50s