[2024-01-24 13:56:27,557] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,559] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3795cfe-438a-474f-9511-f98f1f84a8ac/dqc_reference
[2024-01-24 13:56:28,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,779] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,780] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8cacfe5-f570-4c6a-b8a4-295d2bdcde22/GCF_001263205.1_ASM126320v1_genomic.fna.gz | prodigal -d GCF_001263205.1_ASM126320v1_genomic.fna/cds.fna -a GCF_001263205.1_ASM126320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:05,185] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:05,185] [INFO] Task started: HMMsearch
[2024-01-24 13:57:05,185] [INFO] Running command: hmmsearch --tblout GCF_001263205.1_ASM126320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3795cfe-438a-474f-9511-f98f1f84a8ac/dqc_reference/reference_markers.hmm GCF_001263205.1_ASM126320v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:05,617] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:05,619] [INFO] Found 6/6 markers.
[2024-01-24 13:57:05,710] [INFO] Query marker FASTA was written to GCF_001263205.1_ASM126320v1_genomic.fna/markers.fasta
[2024-01-24 13:57:05,711] [INFO] Task started: Blastn
[2024-01-24 13:57:05,711] [INFO] Running command: blastn -query GCF_001263205.1_ASM126320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3795cfe-438a-474f-9511-f98f1f84a8ac/dqc_reference/reference_markers.fasta -out GCF_001263205.1_ASM126320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:06,467] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:06,471] [INFO] Selected 32 target genomes.
[2024-01-24 13:57:06,472] [INFO] Target genome list was writen to GCF_001263205.1_ASM126320v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:06,498] [INFO] Task started: fastANI
[2024-01-24 13:57:06,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8cacfe5-f570-4c6a-b8a4-295d2bdcde22/GCF_001263205.1_ASM126320v1_genomic.fna.gz --refList GCF_001263205.1_ASM126320v1_genomic.fna/target_genomes.txt --output GCF_001263205.1_ASM126320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:46,850] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:46,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3795cfe-438a-474f-9511-f98f1f84a8ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:46,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3795cfe-438a-474f-9511-f98f1f84a8ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:46,877] [INFO] Found 32 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:46,878] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:46,878] [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
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	100.0	4060	4063	95	conclusive
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	76.0308	708	4063	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.9219	689	4063	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.8529	679	4063	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.7554	421	4063	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	75.6022	52	4063	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.4949	757	4063	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	75.3724	75	4063	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	75.2113	93	4063	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.2094	140	4063	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.1281	149	4063	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	75.0904	128	4063	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	75.0851	117	4063	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	75.0772	63	4063	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	75.0059	223	4063	95	below_threshold
Amycolatopsis benzoatilytica	strain=AK 16/65	GCA_000383915.1	346045	346045	type	True	75.0056	196	4063	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	75.0011	254	4063	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000484675.1	35760	35760	type	True	74.9916	80	4063	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	74.9448	156	4063	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	74.9337	180	4063	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	74.8909	298	4063	95	below_threshold
Burkholderia dolosa	strain=LMG 18943	GCA_902499135.1	152500	152500	type	True	74.8717	261	4063	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	74.8579	234	4063	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	74.8231	316	4063	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	74.8227	217	4063	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	74.819	134	4063	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	74.8176	235	4063	95	below_threshold
Caballeronia arationis		GCA_001544975.2	1777142	1777142	type	True	74.7827	216	4063	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	74.781	263	4063	95	below_threshold
Streptomyces gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	74.7634	249	4063	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	74.7591	318	4063	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	74.7099	306	4063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:46,880] [INFO] DFAST Taxonomy check result was written to GCF_001263205.1_ASM126320v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:46,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:46,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:46,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3795cfe-438a-474f-9511-f98f1f84a8ac/dqc_reference/checkm_data
[2024-01-24 13:57:46,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:46,991] [INFO] Task started: CheckM
[2024-01-24 13:57:46,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001263205.1_ASM126320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001263205.1_ASM126320v1_genomic.fna/checkm_input GCF_001263205.1_ASM126320v1_genomic.fna/checkm_result
[2024-01-24 14:00:03,340] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:03,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:03,402] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:03,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:03,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001263205.1_ASM126320v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:03,404] [INFO] Task started: Blastn
[2024-01-24 14:00:03,404] [INFO] Running command: blastn -query GCF_001263205.1_ASM126320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3795cfe-438a-474f-9511-f98f1f84a8ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_001263205.1_ASM126320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:04,705] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:04,709] [INFO] Selected 16 target genomes.
[2024-01-24 14:00:04,709] [INFO] Target genome list was writen to GCF_001263205.1_ASM126320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:04,782] [INFO] Task started: fastANI
[2024-01-24 14:00:04,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8cacfe5-f570-4c6a-b8a4-295d2bdcde22/GCF_001263205.1_ASM126320v1_genomic.fna.gz --refList GCF_001263205.1_ASM126320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001263205.1_ASM126320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:33,701] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:33,723] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:33,724] [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_001263205.1	s__Labilithrix luteola	100.0	4060	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001899635.1	s__Labilithrix sp001899635	78.6427	1418	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009781005.1	s__Labilithrix sp009781005	77.6286	542	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712525.1	s__JAAFHV01 sp016712525	77.1361	745	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720545.1	s__JAAFHV01 sp016720545	76.901	670	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	99.45	99.45	0.94	0.94	2	-
GCA_009780955.1	s__Labilithrix sp009780955	76.8886	304	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297655.1	s__JAAFHV01 sp013297655	76.701	727	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703425.1	s__JADJCA01 sp016703425	76.5813	592	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777185.1	s__SXNL01 sp005777185	76.4782	555	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SXNL01	95.0	99.91	99.91	0.95	0.95	3	-
GCA_903858055.1	s__CAIQDA01 sp903858055	76.4534	303	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIQDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893335.1	s__CAITLX01 sp903893335	76.1033	488	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709545.1	s__JADJMO01 sp016709545	75.9377	652	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	95.09	95.09	0.90	0.90	2	-
GCF_009649845.1	s__Polyangium spumosum	75.8396	680	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182965.1	s__JADJMO01 sp016182965	75.8288	697	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002950945.1	s__Sorangium cellulosum_E	75.6632	766	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298625.1	s__Ga0077539 sp013298625	75.1724	499	4063	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__Ga0077539	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:33,725] [INFO] GTDB search result was written to GCF_001263205.1_ASM126320v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:33,726] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:33,731] [INFO] DFAST_QC result json was written to GCF_001263205.1_ASM126320v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:33,731] [INFO] DFAST_QC completed!
[2024-01-24 14:00:33,731] [INFO] Total running time: 0h4m6s