[2024-01-24 13:17:34,115] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,119] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg62a60258-9479-4bcb-9e37-e97ecac08a53/dqc_reference
[2024-01-24 13:17:35,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,554] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,555] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa40571f-91c6-47a5-aa94-5170ca4c2142/GCF_014644535.1_ASM1464453v1_genomic.fna.gz | prodigal -d GCF_014644535.1_ASM1464453v1_genomic.fna/cds.fna -a GCF_014644535.1_ASM1464453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:55,707] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:55,708] [INFO] Task started: HMMsearch
[2024-01-24 13:17:55,708] [INFO] Running command: hmmsearch --tblout GCF_014644535.1_ASM1464453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62a60258-9479-4bcb-9e37-e97ecac08a53/dqc_reference/reference_markers.hmm GCF_014644535.1_ASM1464453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:56,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:56,046] [INFO] Found 6/6 markers.
[2024-01-24 13:17:56,100] [INFO] Query marker FASTA was written to GCF_014644535.1_ASM1464453v1_genomic.fna/markers.fasta
[2024-01-24 13:17:56,101] [INFO] Task started: Blastn
[2024-01-24 13:17:56,101] [INFO] Running command: blastn -query GCF_014644535.1_ASM1464453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a60258-9479-4bcb-9e37-e97ecac08a53/dqc_reference/reference_markers.fasta -out GCF_014644535.1_ASM1464453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:56,937] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:56,940] [INFO] Selected 17 target genomes.
[2024-01-24 13:17:56,941] [INFO] Target genome list was writen to GCF_014644535.1_ASM1464453v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:56,943] [INFO] Task started: fastANI
[2024-01-24 13:17:56,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa40571f-91c6-47a5-aa94-5170ca4c2142/GCF_014644535.1_ASM1464453v1_genomic.fna.gz --refList GCF_014644535.1_ASM1464453v1_genomic.fna/target_genomes.txt --output GCF_014644535.1_ASM1464453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:18,151] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:18,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62a60258-9479-4bcb-9e37-e97ecac08a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:18,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62a60258-9479-4bcb-9e37-e97ecac08a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:18,165] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:18,165] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:18,165] [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	100.0	2100	2102	95	conclusive
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	83.0548	1267	2102	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	82.2742	1066	2102	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	82.1881	936	2102	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	79.046	827	2102	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	78.998	889	2102	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	78.8776	839	2102	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	78.8412	832	2102	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	78.5922	807	2102	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.3048	687	2102	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.2851	665	2102	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.2811	624	2102	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.05	668	2102	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.9696	586	2102	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	77.8815	583	2102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:18,168] [INFO] DFAST Taxonomy check result was written to GCF_014644535.1_ASM1464453v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:18,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:18,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:18,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62a60258-9479-4bcb-9e37-e97ecac08a53/dqc_reference/checkm_data
[2024-01-24 13:18:18,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:18,233] [INFO] Task started: CheckM
[2024-01-24 13:18:18,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644535.1_ASM1464453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644535.1_ASM1464453v1_genomic.fna/checkm_input GCF_014644535.1_ASM1464453v1_genomic.fna/checkm_result
[2024-01-24 13:19:25,849] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:25,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,868] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:25,868] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:25,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644535.1_ASM1464453v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:25,869] [INFO] Task started: Blastn
[2024-01-24 13:19:25,869] [INFO] Running command: blastn -query GCF_014644535.1_ASM1464453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a60258-9479-4bcb-9e37-e97ecac08a53/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644535.1_ASM1464453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:27,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:27,337] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:27,337] [INFO] Target genome list was writen to GCF_014644535.1_ASM1464453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:27,352] [INFO] Task started: fastANI
[2024-01-24 13:19:27,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa40571f-91c6-47a5-aa94-5170ca4c2142/GCF_014644535.1_ASM1464453v1_genomic.fna.gz --refList GCF_014644535.1_ASM1464453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644535.1_ASM1464453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:47,409] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:47,422] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:47,422] [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_014644535.1	s__Roseomonas_B lacus	100.0	2100	2102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018129005.1	s__Roseomonas_B eburnea	83.0722	1274	2102	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_012163135.1	s__Roseomonas_B oryzicola	83.0371	1269	2102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018129025.1	s__Roseomonas_B terrae	82.9107	1262	2102	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	82.8116	1015	2102	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_012927745.1	s__Roseomonas_B sp012927745	82.7487	1219	2102	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_018129065.1	s__Roseomonas_B soli	82.6992	1172	2102	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	82.652	1109	2102	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_017813355.1	s__Roseomonas_B sp017813355	82.5839	1157	2102	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_014199195.1	s__Roseomonas_B alkaliterrae	82.2758	1066	2102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_005222755.1	s__Roseomonas_B sp005222755	82.0434	1186	2102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:47,424] [INFO] GTDB search result was written to GCF_014644535.1_ASM1464453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:47,424] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:47,428] [INFO] DFAST_QC result json was written to GCF_014644535.1_ASM1464453v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:47,428] [INFO] DFAST_QC completed!
[2024-01-24 13:19:47,429] [INFO] Total running time: 0h2m13s