[2024-01-24 14:28:18,145] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:18,156] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:18,156] [INFO] DQC Reference Directory: /var/lib/cwl/stg45d06bef-3cde-4cd8-bd51-777e2474a83d/dqc_reference
[2024-01-24 14:28:20,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,480] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg04460254-f24f-447a-ab8e-c7d23de03733/GCF_011040385.1_ASM1104038v1_genomic.fna.gz | prodigal -d GCF_011040385.1_ASM1104038v1_genomic.fna/cds.fna -a GCF_011040385.1_ASM1104038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:40,907] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:40,907] [INFO] Task started: HMMsearch
[2024-01-24 14:28:40,908] [INFO] Running command: hmmsearch --tblout GCF_011040385.1_ASM1104038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45d06bef-3cde-4cd8-bd51-777e2474a83d/dqc_reference/reference_markers.hmm GCF_011040385.1_ASM1104038v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:41,258] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:41,260] [INFO] Found 6/6 markers.
[2024-01-24 14:28:41,321] [INFO] Query marker FASTA was written to GCF_011040385.1_ASM1104038v1_genomic.fna/markers.fasta
[2024-01-24 14:28:41,322] [INFO] Task started: Blastn
[2024-01-24 14:28:41,322] [INFO] Running command: blastn -query GCF_011040385.1_ASM1104038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d06bef-3cde-4cd8-bd51-777e2474a83d/dqc_reference/reference_markers.fasta -out GCF_011040385.1_ASM1104038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:42,272] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:42,277] [INFO] Selected 20 target genomes.
[2024-01-24 14:28:42,278] [INFO] Target genome list was writen to GCF_011040385.1_ASM1104038v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:42,288] [INFO] Task started: fastANI
[2024-01-24 14:28:42,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg04460254-f24f-447a-ab8e-c7d23de03733/GCF_011040385.1_ASM1104038v1_genomic.fna.gz --refList GCF_011040385.1_ASM1104038v1_genomic.fna/target_genomes.txt --output GCF_011040385.1_ASM1104038v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:08,279] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:08,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45d06bef-3cde-4cd8-bd51-777e2474a83d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:08,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45d06bef-3cde-4cd8-bd51-777e2474a83d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:08,303] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:29:08,303] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:29:08,303] [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
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	82.7124	1270	2156	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	82.6216	1334	2156	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	82.3755	1311	2156	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.6035	774	2156	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	79.3391	784	2156	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	79.1459	840	2156	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	78.8651	787	2156	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	78.6675	868	2156	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	78.6402	865	2156	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.6198	716	2156	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	78.5658	849	2156	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	78.5069	783	2156	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	78.4917	684	2156	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	78.4885	781	2156	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	78.3949	671	2156	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.341	835	2156	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.2667	736	2156	95	below_threshold
Roseomonas arctica	strain=LMG 28251	GCA_018128965.1	1509237	1509237	type	True	78.1554	711	2156	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.0887	750	2156	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.8033	611	2156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:08,305] [INFO] DFAST Taxonomy check result was written to GCF_011040385.1_ASM1104038v1_genomic.fna/tc_result.tsv
[2024-01-24 14:29:08,306] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:08,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:08,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45d06bef-3cde-4cd8-bd51-777e2474a83d/dqc_reference/checkm_data
[2024-01-24 14:29:08,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:08,367] [INFO] Task started: CheckM
[2024-01-24 14:29:08,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011040385.1_ASM1104038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011040385.1_ASM1104038v1_genomic.fna/checkm_input GCF_011040385.1_ASM1104038v1_genomic.fna/checkm_result
[2024-01-24 14:31:08,903] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:08,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:08,925] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:08,926] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:08,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011040385.1_ASM1104038v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:08,926] [INFO] Task started: Blastn
[2024-01-24 14:31:08,927] [INFO] Running command: blastn -query GCF_011040385.1_ASM1104038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d06bef-3cde-4cd8-bd51-777e2474a83d/dqc_reference/reference_markers_gtdb.fasta -out GCF_011040385.1_ASM1104038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:10,710] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:10,715] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:10,715] [INFO] Target genome list was writen to GCF_011040385.1_ASM1104038v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:10,725] [INFO] Task started: fastANI
[2024-01-24 14:31:10,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg04460254-f24f-447a-ab8e-c7d23de03733/GCF_011040385.1_ASM1104038v1_genomic.fna.gz --refList GCF_011040385.1_ASM1104038v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011040385.1_ASM1104038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:33,614] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:33,628] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:33,628] [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_011040385.1	s__Roseomonas_A sp011040385	100.0	2154	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016805305.1	s__Roseomonas_A sp016805305	91.9355	1861	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114315.1	s__Roseomonas_A stagni	89.5364	1781	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012103215.1	s__Roseomonas_A sp012103215	82.7154	1269	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019024325.1	s__Roseomonas_A tokyonensis	82.6993	1321	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012163145.1	s__Roseomonas_A frigidaquae	82.349	1314	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019029495.1	s__Roseomonas_A sp019029495	82.3017	1294	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173615.1	s__Roseomonas_A sp003173615	81.2103	1189	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222815.1	s__Roseomonas_A sp005222815	80.9802	1237	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343615.1	s__Paracraurococcus sp004343615	79.0473	929	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355005.1	s__Paracraurococcus ruber_A	78.8323	952	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:33,635] [INFO] GTDB search result was written to GCF_011040385.1_ASM1104038v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:33,636] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:33,642] [INFO] DFAST_QC result json was written to GCF_011040385.1_ASM1104038v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:33,642] [INFO] DFAST_QC completed!
[2024-01-24 14:31:33,642] [INFO] Total running time: 0h3m15s