[2024-01-24 12:40:07,945] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,948] [INFO] DQC Reference Directory: /var/lib/cwl/stg3486c393-632a-4d42-9f65-5c4b3dc1ccb9/dqc_reference
[2024-01-24 12:40:09,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,429] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,430] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7f9888c-0e89-4fd2-b606-6067173d3acc/GCF_000202835.1_ASM20283v1_genomic.fna.gz | prodigal -d GCF_000202835.1_ASM20283v1_genomic.fna/cds.fna -a GCF_000202835.1_ASM20283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:21,780] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:21,780] [INFO] Task started: HMMsearch
[2024-01-24 12:40:21,780] [INFO] Running command: hmmsearch --tblout GCF_000202835.1_ASM20283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3486c393-632a-4d42-9f65-5c4b3dc1ccb9/dqc_reference/reference_markers.hmm GCF_000202835.1_ASM20283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:22,071] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:22,073] [INFO] Found 6/6 markers.
[2024-01-24 12:40:22,125] [INFO] Query marker FASTA was written to GCF_000202835.1_ASM20283v1_genomic.fna/markers.fasta
[2024-01-24 12:40:22,129] [INFO] Task started: Blastn
[2024-01-24 12:40:22,129] [INFO] Running command: blastn -query GCF_000202835.1_ASM20283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3486c393-632a-4d42-9f65-5c4b3dc1ccb9/dqc_reference/reference_markers.fasta -out GCF_000202835.1_ASM20283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:23,135] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:23,138] [INFO] Selected 17 target genomes.
[2024-01-24 12:40:23,139] [INFO] Target genome list was writen to GCF_000202835.1_ASM20283v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:23,155] [INFO] Task started: fastANI
[2024-01-24 12:40:23,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7f9888c-0e89-4fd2-b606-6067173d3acc/GCF_000202835.1_ASM20283v1_genomic.fna.gz --refList GCF_000202835.1_ASM20283v1_genomic.fna/target_genomes.txt --output GCF_000202835.1_ASM20283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:39,968] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:39,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3486c393-632a-4d42-9f65-5c4b3dc1ccb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:39,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3486c393-632a-4d42-9f65-5c4b3dc1ccb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:39,986] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:39,986] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:39,986] [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
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	100.0	1398	1400	95	conclusive
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	99.6573	1060	1400	95	conclusive
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	80.8174	636	1400	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.1065	280	1400	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.6439	441	1400	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.5073	382	1400	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.3799	392	1400	95	below_threshold
Acidibrevibacterium fodinaquatile	strain=G45-3	GCA_003352165.1	1969806	1969806	type	True	77.3766	346	1400	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	77.2911	283	1400	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	77.1922	407	1400	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	77.154	387	1400	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	77.0996	319	1400	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.914	276	1400	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	76.9124	391	1400	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.8978	301	1400	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	76.7857	313	1400	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.0036	183	1400	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:39,989] [INFO] DFAST Taxonomy check result was written to GCF_000202835.1_ASM20283v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:39,989] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:39,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:39,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3486c393-632a-4d42-9f65-5c4b3dc1ccb9/dqc_reference/checkm_data
[2024-01-24 12:40:39,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:40,036] [INFO] Task started: CheckM
[2024-01-24 12:40:40,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000202835.1_ASM20283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000202835.1_ASM20283v1_genomic.fna/checkm_input GCF_000202835.1_ASM20283v1_genomic.fna/checkm_result
[2024-01-24 12:41:25,152] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:25,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:25,172] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:25,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:25,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000202835.1_ASM20283v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:25,173] [INFO] Task started: Blastn
[2024-01-24 12:41:25,173] [INFO] Running command: blastn -query GCF_000202835.1_ASM20283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3486c393-632a-4d42-9f65-5c4b3dc1ccb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000202835.1_ASM20283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:26,958] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:26,962] [INFO] Selected 18 target genomes.
[2024-01-24 12:41:26,963] [INFO] Target genome list was writen to GCF_000202835.1_ASM20283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:26,977] [INFO] Task started: fastANI
[2024-01-24 12:41:26,977] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7f9888c-0e89-4fd2-b606-6067173d3acc/GCF_000202835.1_ASM20283v1_genomic.fna.gz --refList GCF_000202835.1_ASM20283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000202835.1_ASM20283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:43,415] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:43,441] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:43,442] [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_000202835.1	s__Acidiphilium multivorum	100.0	1399	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	conclusive
GCF_902712915.1	s__Acidiphilium sp002255515	89.4769	888	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.59	99.19	0.97	0.94	3	-
GCF_900156265.1	s__Acidiphilium rubrum	79.2302	564	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	97.80	96.68	0.89	0.85	4	-
GCA_003133265.1	s__PALSA-911 sp003133265	77.7085	267	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	77.6493	338	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	77.5755	387	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	77.5302	351	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928895.1	s__CAIYPH01 sp903928895	77.3161	315	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	99.93	99.91	0.97	0.97	4	-
GCA_002279355.1	s__Acidiphilium sp002279355	77.2066	243	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.80	99.77	0.93	0.92	3	-
GCF_002937115.1	s__Rhodopila globiformis	77.1565	388	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011332665.1	s__Acidibrevibacterium sp011332665	77.1394	255	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidibrevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	77.0219	366	1400	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	76.9214	415	1400	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_006438825.1	s__Roseomonas nepalensis	76.8719	368	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928045.1	s__CAIYPH01 sp903928045	76.8417	246	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	98.55	98.55	0.76	0.76	2	-
GCF_000711725.1	s__Roseomonas aerilata	76.8007	311	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107305.1	s__Roseomonas sp016107305	76.7708	308	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845065.1	s__CAIYPH01 sp903845065	76.76	329	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:43,444] [INFO] GTDB search result was written to GCF_000202835.1_ASM20283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:43,445] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:43,451] [INFO] DFAST_QC result json was written to GCF_000202835.1_ASM20283v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:43,451] [INFO] DFAST_QC completed!
[2024-01-24 12:41:43,452] [INFO] Total running time: 0h1m36s