[2023-06-27 16:01:22,091] [INFO] DFAST_QC pipeline started.
[2023-06-27 16:01:22,093] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 16:01:22,093] [INFO] DQC Reference Directory: /var/lib/cwl/stg933065dc-72aa-471d-b9fe-f659d0fc0ffc/dqc_reference
[2023-06-27 16:01:23,267] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 16:01:23,268] [INFO] Task started: Prodigal
[2023-06-27 16:01:23,268] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b7c2306-272c-42a8-a0ec-00abc0da7ecf/GCA_026647795.1_ASM2664779v1_genomic.fna.gz | prodigal -d GCA_026647795.1_ASM2664779v1_genomic.fna/cds.fna -a GCA_026647795.1_ASM2664779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 16:01:40,951] [INFO] Task succeeded: Prodigal
[2023-06-27 16:01:40,952] [INFO] Task started: HMMsearch
[2023-06-27 16:01:40,952] [INFO] Running command: hmmsearch --tblout GCA_026647795.1_ASM2664779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg933065dc-72aa-471d-b9fe-f659d0fc0ffc/dqc_reference/reference_markers.hmm GCA_026647795.1_ASM2664779v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 16:01:41,225] [INFO] Task succeeded: HMMsearch
[2023-06-27 16:01:41,226] [INFO] Found 6/6 markers.
[2023-06-27 16:01:41,290] [INFO] Query marker FASTA was written to GCA_026647795.1_ASM2664779v1_genomic.fna/markers.fasta
[2023-06-27 16:01:41,290] [INFO] Task started: Blastn
[2023-06-27 16:01:41,290] [INFO] Running command: blastn -query GCA_026647795.1_ASM2664779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg933065dc-72aa-471d-b9fe-f659d0fc0ffc/dqc_reference/reference_markers.fasta -out GCA_026647795.1_ASM2664779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 16:01:41,967] [INFO] Task succeeded: Blastn
[2023-06-27 16:01:41,970] [INFO] Selected 25 target genomes.
[2023-06-27 16:01:41,971] [INFO] Target genome list was writen to GCA_026647795.1_ASM2664779v1_genomic.fna/target_genomes.txt
[2023-06-27 16:01:41,974] [INFO] Task started: fastANI
[2023-06-27 16:01:41,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b7c2306-272c-42a8-a0ec-00abc0da7ecf/GCA_026647795.1_ASM2664779v1_genomic.fna.gz --refList GCA_026647795.1_ASM2664779v1_genomic.fna/target_genomes.txt --output GCA_026647795.1_ASM2664779v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 16:02:05,854] [INFO] Task succeeded: fastANI
[2023-06-27 16:02:05,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg933065dc-72aa-471d-b9fe-f659d0fc0ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 16:02:05,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg933065dc-72aa-471d-b9fe-f659d0fc0ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 16:02:05,875] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 16:02:05,875] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 16:02:05,875] [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
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.5838	434	1953	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.4717	215	1953	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.4039	379	1953	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.295	357	1953	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.2862	260	1953	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.2103	108	1953	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	75.0465	133	1953	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	74.9833	166	1953	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	74.9816	151	1953	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	74.9742	139	1953	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	74.9705	123	1953	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	74.9528	139	1953	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.9414	206	1953	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	74.9163	165	1953	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	74.9157	123	1953	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	74.8803	144	1953	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	74.8746	145	1953	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	74.8498	149	1953	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	74.8182	138	1953	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	74.7956	158	1953	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	74.7907	177	1953	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	74.7878	86	1953	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	74.7439	346	1953	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	74.7426	349	1953	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	74.6722	229	1953	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 16:02:05,878] [INFO] DFAST Taxonomy check result was written to GCA_026647795.1_ASM2664779v1_genomic.fna/tc_result.tsv
[2023-06-27 16:02:05,879] [INFO] ===== Taxonomy check completed =====
[2023-06-27 16:02:05,879] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 16:02:05,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg933065dc-72aa-471d-b9fe-f659d0fc0ffc/dqc_reference/checkm_data
[2023-06-27 16:02:05,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 16:02:05,943] [INFO] Task started: CheckM
[2023-06-27 16:02:05,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026647795.1_ASM2664779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026647795.1_ASM2664779v1_genomic.fna/checkm_input GCA_026647795.1_ASM2664779v1_genomic.fna/checkm_result
[2023-06-27 16:03:08,774] [INFO] Task succeeded: CheckM
[2023-06-27 16:03:08,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 16:03:08,799] [INFO] ===== Completeness check finished =====
[2023-06-27 16:03:08,799] [INFO] ===== Start GTDB Search =====
[2023-06-27 16:03:08,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026647795.1_ASM2664779v1_genomic.fna/markers.fasta)
[2023-06-27 16:03:08,800] [INFO] Task started: Blastn
[2023-06-27 16:03:08,800] [INFO] Running command: blastn -query GCA_026647795.1_ASM2664779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg933065dc-72aa-471d-b9fe-f659d0fc0ffc/dqc_reference/reference_markers_gtdb.fasta -out GCA_026647795.1_ASM2664779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 16:03:09,848] [INFO] Task succeeded: Blastn
[2023-06-27 16:03:09,852] [INFO] Selected 12 target genomes.
[2023-06-27 16:03:09,852] [INFO] Target genome list was writen to GCA_026647795.1_ASM2664779v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 16:03:09,858] [INFO] Task started: fastANI
[2023-06-27 16:03:09,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b7c2306-272c-42a8-a0ec-00abc0da7ecf/GCA_026647795.1_ASM2664779v1_genomic.fna.gz --refList GCA_026647795.1_ASM2664779v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026647795.1_ASM2664779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 16:03:27,616] [INFO] Task succeeded: fastANI
[2023-06-27 16:03:27,627] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 16:03:27,627] [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_016191785.1	s__JADJKB01 sp016191785	85.8067	1625	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075635.1	s__JADJKB01 sp015075635	81.1019	1362	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJKB01	95.0	96.31	96.31	0.86	0.86	2	-
GCA_016706225.1	s__JADJKB01 sp016706225	78.7492	1026	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514535.1	s__NIC37A-2 sp012514535	76.1686	240	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__NIC37A-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193285.1	s__PMG-095 sp004193285	76.0525	289	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__PMG-095	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893335.1	s__CAITLX01 sp903893335	75.8188	331	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218915.1	s__JACRCQ01 sp016218915	75.6912	185	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRCQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709545.1	s__JADJMO01 sp016709545	75.5787	393	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	95.09	95.09	0.90	0.90	2	-
GCA_001899635.1	s__Labilithrix sp001899635	75.3982	296	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067165.1	s__Sorangium cellulosum_B	75.2638	441	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	75.2585	551	1953	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_003242475.1	s__ZC4RG40 sp003242475	74.9676	75	1953	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__ZC4RG40	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 16:03:27,629] [INFO] GTDB search result was written to GCA_026647795.1_ASM2664779v1_genomic.fna/result_gtdb.tsv
[2023-06-27 16:03:27,630] [INFO] ===== GTDB Search completed =====
[2023-06-27 16:03:27,634] [INFO] DFAST_QC result json was written to GCA_026647795.1_ASM2664779v1_genomic.fna/dqc_result.json
[2023-06-27 16:03:27,634] [INFO] DFAST_QC completed!
[2023-06-27 16:03:27,634] [INFO] Total running time: 0h2m6s