[2023-06-28 12:00:02,197] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:00:02,200] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:00:02,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cdb0394-8c90-49ee-8e17-cd247f27ac2c/dqc_reference
[2023-06-28 12:00:03,484] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:00:03,485] [INFO] Task started: Prodigal
[2023-06-28 12:00:03,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg585e1d1c-60e6-4bf6-b41b-55213ffa37b2/GCA_027482185.1_ASM2748218v1_genomic.fna.gz | prodigal -d GCA_027482185.1_ASM2748218v1_genomic.fna/cds.fna -a GCA_027482185.1_ASM2748218v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:00:40,694] [INFO] Task succeeded: Prodigal
[2023-06-28 12:00:40,695] [INFO] Task started: HMMsearch
[2023-06-28 12:00:40,695] [INFO] Running command: hmmsearch --tblout GCA_027482185.1_ASM2748218v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cdb0394-8c90-49ee-8e17-cd247f27ac2c/dqc_reference/reference_markers.hmm GCA_027482185.1_ASM2748218v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:00:41,005] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:00:41,007] [INFO] Found 6/6 markers.
[2023-06-28 12:00:41,059] [INFO] Query marker FASTA was written to GCA_027482185.1_ASM2748218v1_genomic.fna/markers.fasta
[2023-06-28 12:00:41,059] [INFO] Task started: Blastn
[2023-06-28 12:00:41,060] [INFO] Running command: blastn -query GCA_027482185.1_ASM2748218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cdb0394-8c90-49ee-8e17-cd247f27ac2c/dqc_reference/reference_markers.fasta -out GCA_027482185.1_ASM2748218v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:00:41,677] [INFO] Task succeeded: Blastn
[2023-06-28 12:00:41,682] [INFO] Selected 11 target genomes.
[2023-06-28 12:00:41,683] [INFO] Target genome list was writen to GCA_027482185.1_ASM2748218v1_genomic.fna/target_genomes.txt
[2023-06-28 12:00:41,684] [INFO] Task started: fastANI
[2023-06-28 12:00:41,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg585e1d1c-60e6-4bf6-b41b-55213ffa37b2/GCA_027482185.1_ASM2748218v1_genomic.fna.gz --refList GCA_027482185.1_ASM2748218v1_genomic.fna/target_genomes.txt --output GCA_027482185.1_ASM2748218v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:00:50,570] [INFO] Task succeeded: fastANI
[2023-06-28 12:00:50,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cdb0394-8c90-49ee-8e17-cd247f27ac2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:00:50,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cdb0394-8c90-49ee-8e17-cd247f27ac2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:00:50,582] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:00:50,582] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:00:50,582] [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
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	78.0543	314	2131	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.8773	407	2131	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.7795	467	2131	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.6316	222	2131	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	77.2956	248	2131	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	77.1764	262	2131	95	below_threshold
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	76.9052	149	2131	95	below_threshold
Ruficoccus amylovorans	strain=JCM31066	GCA_014230085.1	1804625	1804625	type	True	76.1918	118	2131	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	74.655	114	2131	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:00:50,584] [INFO] DFAST Taxonomy check result was written to GCA_027482185.1_ASM2748218v1_genomic.fna/tc_result.tsv
[2023-06-28 12:00:50,585] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:00:50,585] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:00:50,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cdb0394-8c90-49ee-8e17-cd247f27ac2c/dqc_reference/checkm_data
[2023-06-28 12:00:50,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:00:50,649] [INFO] Task started: CheckM
[2023-06-28 12:00:50,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027482185.1_ASM2748218v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027482185.1_ASM2748218v1_genomic.fna/checkm_input GCA_027482185.1_ASM2748218v1_genomic.fna/checkm_result
[2023-06-28 12:02:37,566] [INFO] Task succeeded: CheckM
[2023-06-28 12:02:37,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:02:37,592] [INFO] ===== Completeness check finished =====
[2023-06-28 12:02:37,592] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:02:37,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027482185.1_ASM2748218v1_genomic.fna/markers.fasta)
[2023-06-28 12:02:37,593] [INFO] Task started: Blastn
[2023-06-28 12:02:37,594] [INFO] Running command: blastn -query GCA_027482185.1_ASM2748218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cdb0394-8c90-49ee-8e17-cd247f27ac2c/dqc_reference/reference_markers_gtdb.fasta -out GCA_027482185.1_ASM2748218v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:38,522] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:38,528] [INFO] Selected 23 target genomes.
[2023-06-28 12:02:38,528] [INFO] Target genome list was writen to GCA_027482185.1_ASM2748218v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:02:38,542] [INFO] Task started: fastANI
[2023-06-28 12:02:38,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg585e1d1c-60e6-4bf6-b41b-55213ffa37b2/GCA_027482185.1_ASM2748218v1_genomic.fna.gz --refList GCA_027482185.1_ASM2748218v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027482185.1_ASM2748218v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:03:01,744] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:01,842] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:03:01,845] [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_002288455.1	s__ER46 sp002288455	88.4264	1164	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794785.1	s__ER46 sp016794785	79.8106	900	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903948415.1	s__CAITWF01 sp903948415	79.591	786	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794665.1	s__ER46 sp016794665	79.5605	785	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235555.1	s__ER46 sp016235555	79.5532	941	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793535.1	s__ER46 sp016793535	79.3813	806	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903825285.1	s__Opi-474 sp903825285	79.1721	520	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.78	99.55	0.96	0.94	12	-
GCA_016715765.1	s__UBA2377 sp016715765	79.0441	429	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872505.1	s__Opi-474 sp903872505	78.8992	453	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCA_903820035.1	s__ER46 sp903820035	78.7697	669	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.61	99.58	0.90	0.89	3	-
GCA_903902745.1	s__CAIUWA01 sp903902745	78.7531	406	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIUWA01	95.0	99.98	99.98	0.98	0.97	4	-
GCF_003054705.1	s__ER46 sp003054705	78.653	578	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746835.1	s__Lacunisphaera limnophila	78.6056	477	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900845.1	s__ER46 sp903900845	78.5862	599	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187925.1	s__Didemnitutus sp016187925	78.5557	455	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877135.1	s__Opitutus sp903877135	78.4658	437	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	99.97	99.95	0.97	0.97	4	-
GCA_002304445.1	s__Tous-C4FEB sp002304445	78.1747	459	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	98.22	97.15	0.85	0.81	4	-
GCF_007559335.1	s__Rariglobus hedericola	78.1491	305	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898675.1	s__Lacunisphaera sp903898675	78.1344	357	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	99.99	99.98	0.99	0.98	5	-
GCA_903876795.1	s__Rariglobus sp903876795	78.1303	329	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904685.1	s__Rariglobus sp903904685	78.0336	301	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	99.84	99.84	0.96	0.96	2	-
GCA_005792355.1	s__ER46 sp005792355	78.0063	727	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.97	99.97	0.97	0.97	2	-
GCA_002737275.1	s__Tous-C4FEB sp002737275	77.7725	327	2131	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:03:01,867] [INFO] GTDB search result was written to GCA_027482185.1_ASM2748218v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:03:01,871] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:03:01,934] [INFO] DFAST_QC result json was written to GCA_027482185.1_ASM2748218v1_genomic.fna/dqc_result.json
[2023-06-28 12:03:01,936] [INFO] DFAST_QC completed!
[2023-06-28 12:03:01,937] [INFO] Total running time: 0h2m60s