[2023-06-28 12:00:31,315] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:00:31,317] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:00:31,317] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd67281b-f7bd-4b54-ab2c-27fdc382a87b/dqc_reference
[2023-06-28 12:00:32,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:00:32,576] [INFO] Task started: Prodigal
[2023-06-28 12:00:32,576] [INFO] Running command: gunzip -c /var/lib/cwl/stgfac80891-7afa-49a1-a793-defe1bb9eccb/GCA_020249825.1_ASM2024982v1_genomic.fna.gz | prodigal -d GCA_020249825.1_ASM2024982v1_genomic.fna/cds.fna -a GCA_020249825.1_ASM2024982v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:00:45,409] [INFO] Task succeeded: Prodigal
[2023-06-28 12:00:45,409] [INFO] Task started: HMMsearch
[2023-06-28 12:00:45,409] [INFO] Running command: hmmsearch --tblout GCA_020249825.1_ASM2024982v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd67281b-f7bd-4b54-ab2c-27fdc382a87b/dqc_reference/reference_markers.hmm GCA_020249825.1_ASM2024982v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:00:45,755] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:00:45,757] [INFO] Found 6/6 markers.
[2023-06-28 12:00:45,806] [INFO] Query marker FASTA was written to GCA_020249825.1_ASM2024982v1_genomic.fna/markers.fasta
[2023-06-28 12:00:45,807] [INFO] Task started: Blastn
[2023-06-28 12:00:45,807] [INFO] Running command: blastn -query GCA_020249825.1_ASM2024982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd67281b-f7bd-4b54-ab2c-27fdc382a87b/dqc_reference/reference_markers.fasta -out GCA_020249825.1_ASM2024982v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:00:46,697] [INFO] Task succeeded: Blastn
[2023-06-28 12:00:46,702] [INFO] Selected 28 target genomes.
[2023-06-28 12:00:46,703] [INFO] Target genome list was writen to GCA_020249825.1_ASM2024982v1_genomic.fna/target_genomes.txt
[2023-06-28 12:00:46,708] [INFO] Task started: fastANI
[2023-06-28 12:00:46,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgfac80891-7afa-49a1-a793-defe1bb9eccb/GCA_020249825.1_ASM2024982v1_genomic.fna.gz --refList GCA_020249825.1_ASM2024982v1_genomic.fna/target_genomes.txt --output GCA_020249825.1_ASM2024982v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:01:08,906] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:08,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd67281b-f7bd-4b54-ab2c-27fdc382a87b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:01:08,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd67281b-f7bd-4b54-ab2c-27fdc382a87b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:01:08,926] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:01:08,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:01:08,926] [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
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	77.0436	344	1174	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.0379	319	1174	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.901	330	1174	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	76.8906	323	1174	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.633	157	1174	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	76.6011	185	1174	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.522	282	1174	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	76.5182	325	1174	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	76.4755	301	1174	95	below_threshold
Roseomonas arctica	strain=LMG 28251	GCA_018128965.1	1509237	1509237	type	True	76.425	201	1174	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.4191	224	1174	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	76.3927	169	1174	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	76.367	196	1174	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	76.3443	265	1174	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	76.3339	270	1174	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	76.3244	211	1174	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	76.2903	146	1174	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	76.2379	147	1174	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	76.0717	146	1174	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	76.0605	191	1174	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	76.05	148	1174	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	76.0241	153	1174	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.9621	171	1174	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	75.6189	144	1174	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:01:08,928] [INFO] DFAST Taxonomy check result was written to GCA_020249825.1_ASM2024982v1_genomic.fna/tc_result.tsv
[2023-06-28 12:01:08,928] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:01:08,929] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:01:08,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd67281b-f7bd-4b54-ab2c-27fdc382a87b/dqc_reference/checkm_data
[2023-06-28 12:01:08,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:01:08,970] [INFO] Task started: CheckM
[2023-06-28 12:01:08,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020249825.1_ASM2024982v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020249825.1_ASM2024982v1_genomic.fna/checkm_input GCA_020249825.1_ASM2024982v1_genomic.fna/checkm_result
[2023-06-28 12:01:49,664] [INFO] Task succeeded: CheckM
[2023-06-28 12:01:49,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.13%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 12:01:49,688] [INFO] ===== Completeness check finished =====
[2023-06-28 12:01:49,689] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:01:49,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020249825.1_ASM2024982v1_genomic.fna/markers.fasta)
[2023-06-28 12:01:49,691] [INFO] Task started: Blastn
[2023-06-28 12:01:49,691] [INFO] Running command: blastn -query GCA_020249825.1_ASM2024982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd67281b-f7bd-4b54-ab2c-27fdc382a87b/dqc_reference/reference_markers_gtdb.fasta -out GCA_020249825.1_ASM2024982v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:50,926] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:50,929] [INFO] Selected 10 target genomes.
[2023-06-28 12:01:50,929] [INFO] Target genome list was writen to GCA_020249825.1_ASM2024982v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:01:50,935] [INFO] Task started: fastANI
[2023-06-28 12:01:50,935] [INFO] Running command: fastANI --query /var/lib/cwl/stgfac80891-7afa-49a1-a793-defe1bb9eccb/GCA_020249825.1_ASM2024982v1_genomic.fna.gz --refList GCA_020249825.1_ASM2024982v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020249825.1_ASM2024982v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:02:00,075] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:00,086] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:02:00,087] [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_903927465.1	s__Roseomonas_B sp903927465	87.6741	849	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	95.83	95.83	0.91	0.91	2	-
GCA_016869735.1	s__Roseomonas_B sp016869735	87.3485	824	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869715.1	s__Roseomonas_B sp016869715	86.7037	838	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844785.1	s__Roseomonas_B sp903844785	86.4351	681	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	77.2206	343	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	77.0714	336	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106015.1	s__Roseomonas_B sp016106015	77.0451	318	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644535.1	s__Roseomonas_B lacus	77.0437	344	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464375.1	s__Roseomonas_B sp001464375	76.9406	348	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222755.1	s__Roseomonas_B sp005222755	76.8802	347	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:02:00,090] [INFO] GTDB search result was written to GCA_020249825.1_ASM2024982v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:02:00,090] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:02:00,096] [INFO] DFAST_QC result json was written to GCA_020249825.1_ASM2024982v1_genomic.fna/dqc_result.json
[2023-06-28 12:02:00,096] [INFO] DFAST_QC completed!
[2023-06-28 12:02:00,096] [INFO] Total running time: 0h1m29s