[2024-01-24 14:12:31,842] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:31,848] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:31,849] [INFO] DQC Reference Directory: /var/lib/cwl/stg517fbaaf-e84d-4d91-92ec-54a8638dc340/dqc_reference
[2024-01-24 14:12:33,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:33,152] [INFO] Task started: Prodigal
[2024-01-24 14:12:33,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg68e82efe-45f9-4ec4-ae4b-66f78616d39e/GCF_000964345.1_ASM96434v1_genomic.fna.gz | prodigal -d GCF_000964345.1_ASM96434v1_genomic.fna/cds.fna -a GCF_000964345.1_ASM96434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:43,251] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:43,251] [INFO] Task started: HMMsearch
[2024-01-24 14:12:43,251] [INFO] Running command: hmmsearch --tblout GCF_000964345.1_ASM96434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg517fbaaf-e84d-4d91-92ec-54a8638dc340/dqc_reference/reference_markers.hmm GCF_000964345.1_ASM96434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:43,552] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:43,554] [INFO] Found 6/6 markers.
[2024-01-24 14:12:43,598] [INFO] Query marker FASTA was written to GCF_000964345.1_ASM96434v1_genomic.fna/markers.fasta
[2024-01-24 14:12:43,599] [INFO] Task started: Blastn
[2024-01-24 14:12:43,599] [INFO] Running command: blastn -query GCF_000964345.1_ASM96434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg517fbaaf-e84d-4d91-92ec-54a8638dc340/dqc_reference/reference_markers.fasta -out GCF_000964345.1_ASM96434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:44,552] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:44,556] [INFO] Selected 17 target genomes.
[2024-01-24 14:12:44,556] [INFO] Target genome list was writen to GCF_000964345.1_ASM96434v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:44,570] [INFO] Task started: fastANI
[2024-01-24 14:12:44,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg68e82efe-45f9-4ec4-ae4b-66f78616d39e/GCF_000964345.1_ASM96434v1_genomic.fna.gz --refList GCF_000964345.1_ASM96434v1_genomic.fna/target_genomes.txt --output GCF_000964345.1_ASM96434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:00,127] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:00,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg517fbaaf-e84d-4d91-92ec-54a8638dc340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:00,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg517fbaaf-e84d-4d91-92ec-54a8638dc340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:00,142] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:13:00,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:00,142] [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_000964345.1	62140	62140	type	True	100.0	1065	1072	95	conclusive
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	99.9895	1070	1072	95	conclusive
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	80.8579	585	1072	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.181	250	1072	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.84	321	1072	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.8109	367	1072	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.6111	339	1072	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	77.4496	232	1072	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	77.3197	271	1072	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	77.2731	329	1072	95	below_threshold
Acidibrevibacterium fodinaquatile	strain=G45-3	GCA_003352165.1	1969806	1969806	type	True	77.269	289	1072	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	77.2437	354	1072	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	77.1956	336	1072	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	77.1053	248	1072	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	77.0299	243	1072	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	77.0105	265	1072	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.1736	154	1072	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:00,152] [INFO] DFAST Taxonomy check result was written to GCF_000964345.1_ASM96434v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:00,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:00,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:00,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg517fbaaf-e84d-4d91-92ec-54a8638dc340/dqc_reference/checkm_data
[2024-01-24 14:13:00,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:00,202] [INFO] Task started: CheckM
[2024-01-24 14:13:00,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000964345.1_ASM96434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000964345.1_ASM96434v1_genomic.fna/checkm_input GCF_000964345.1_ASM96434v1_genomic.fna/checkm_result
[2024-01-24 14:13:35,546] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:35,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:35,568] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:35,568] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:35,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000964345.1_ASM96434v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:35,569] [INFO] Task started: Blastn
[2024-01-24 14:13:35,569] [INFO] Running command: blastn -query GCF_000964345.1_ASM96434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg517fbaaf-e84d-4d91-92ec-54a8638dc340/dqc_reference/reference_markers_gtdb.fasta -out GCF_000964345.1_ASM96434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:37,388] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:37,393] [INFO] Selected 18 target genomes.
[2024-01-24 14:13:37,393] [INFO] Target genome list was writen to GCF_000964345.1_ASM96434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:37,455] [INFO] Task started: fastANI
[2024-01-24 14:13:37,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg68e82efe-45f9-4ec4-ae4b-66f78616d39e/GCF_000964345.1_ASM96434v1_genomic.fna.gz --refList GCF_000964345.1_ASM96434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000964345.1_ASM96434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:53,851] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:53,871] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:53,872] [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	99.9895	1070	1072	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	89.3646	745	1072	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	79.4332	495	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	97.80	96.68	0.89	0.85	4	-
GCA_017304945.1	s__69-11 sp017304945	77.9912	337	1072	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_003133265.1	s__PALSA-911 sp003133265	77.9361	234	1072	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_018240635.1	s__JAFEFJ01 sp018240635	77.8691	291	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	77.8314	305	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	77.4657	295	1072	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_903928895.1	s__CAIYPH01 sp903928895	77.3143	282	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	99.93	99.91	0.97	0.97	4	-
GCA_011332665.1	s__Acidibrevibacterium sp011332665	77.3125	234	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidibrevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002937115.1	s__Rhodopila globiformis	77.2764	327	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	77.2554	353	1072	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_002279355.1	s__Acidiphilium sp002279355	77.2417	205	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.80	99.77	0.93	0.92	3	-
GCF_006438825.1	s__Roseomonas nepalensis	77.0543	310	1072	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	77.0067	219	1072	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	76.9925	267	1072	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	76.8835	261	1072	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	76.8175	276	1072	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 14:13:53,875] [INFO] GTDB search result was written to GCF_000964345.1_ASM96434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:53,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:53,880] [INFO] DFAST_QC result json was written to GCF_000964345.1_ASM96434v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:53,880] [INFO] DFAST_QC completed!
[2024-01-24 14:13:53,880] [INFO] Total running time: 0h1m22s