[2024-01-24 10:49:34,705] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,707] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,707] [INFO] DQC Reference Directory: /var/lib/cwl/stga383687a-63bf-414f-adae-4ac4a6a8a32b/dqc_reference
[2024-01-24 10:49:35,923] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,924] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,925] [INFO] Running command: gunzip -c /var/lib/cwl/stga4cc4ff2-13e2-46ed-8fde-3bc8b6e29a0f/GCF_014197855.1_ASM1419785v1_genomic.fna.gz | prodigal -d GCF_014197855.1_ASM1419785v1_genomic.fna/cds.fna -a GCF_014197855.1_ASM1419785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:49,691] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:49,692] [INFO] Task started: HMMsearch
[2024-01-24 10:49:49,692] [INFO] Running command: hmmsearch --tblout GCF_014197855.1_ASM1419785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga383687a-63bf-414f-adae-4ac4a6a8a32b/dqc_reference/reference_markers.hmm GCF_014197855.1_ASM1419785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:50,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:50,036] [INFO] Found 6/6 markers.
[2024-01-24 10:49:50,076] [INFO] Query marker FASTA was written to GCF_014197855.1_ASM1419785v1_genomic.fna/markers.fasta
[2024-01-24 10:49:50,076] [INFO] Task started: Blastn
[2024-01-24 10:49:50,077] [INFO] Running command: blastn -query GCF_014197855.1_ASM1419785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga383687a-63bf-414f-adae-4ac4a6a8a32b/dqc_reference/reference_markers.fasta -out GCF_014197855.1_ASM1419785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:50,910] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:50,913] [INFO] Selected 17 target genomes.
[2024-01-24 10:49:50,913] [INFO] Target genome list was writen to GCF_014197855.1_ASM1419785v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:50,920] [INFO] Task started: fastANI
[2024-01-24 10:49:50,920] [INFO] Running command: fastANI --query /var/lib/cwl/stga4cc4ff2-13e2-46ed-8fde-3bc8b6e29a0f/GCF_014197855.1_ASM1419785v1_genomic.fna.gz --refList GCF_014197855.1_ASM1419785v1_genomic.fna/target_genomes.txt --output GCF_014197855.1_ASM1419785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:08,238] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:08,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga383687a-63bf-414f-adae-4ac4a6a8a32b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:08,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga383687a-63bf-414f-adae-4ac4a6a8a32b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:08,259] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:50:08,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:50:08,260] [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
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	100.0	1509	1510	95	conclusive
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	99.9975	1503	1510	95	conclusive
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	99.9931	1487	1510	95	conclusive
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	81.8199	813	1510	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	80.5313	759	1510	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.8717	324	1510	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.6381	146	1510	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.5707	215	1510	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.4363	257	1510	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.2767	214	1510	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.2503	172	1510	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	76.1199	90	1510	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.0668	223	1510	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.0591	165	1510	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.0311	246	1510	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	75.9568	102	1510	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.8001	261	1510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:08,261] [INFO] DFAST Taxonomy check result was written to GCF_014197855.1_ASM1419785v1_genomic.fna/tc_result.tsv
[2024-01-24 10:50:08,262] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:08,262] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:08,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga383687a-63bf-414f-adae-4ac4a6a8a32b/dqc_reference/checkm_data
[2024-01-24 10:50:08,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:08,305] [INFO] Task started: CheckM
[2024-01-24 10:50:08,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197855.1_ASM1419785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197855.1_ASM1419785v1_genomic.fna/checkm_input GCF_014197855.1_ASM1419785v1_genomic.fna/checkm_result
[2024-01-24 10:50:52,666] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:52,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:52,695] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:52,695] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:52,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197855.1_ASM1419785v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:52,696] [INFO] Task started: Blastn
[2024-01-24 10:50:52,696] [INFO] Running command: blastn -query GCF_014197855.1_ASM1419785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga383687a-63bf-414f-adae-4ac4a6a8a32b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197855.1_ASM1419785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:54,108] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:54,112] [INFO] Selected 11 target genomes.
[2024-01-24 10:50:54,112] [INFO] Target genome list was writen to GCF_014197855.1_ASM1419785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:54,157] [INFO] Task started: fastANI
[2024-01-24 10:50:54,157] [INFO] Running command: fastANI --query /var/lib/cwl/stga4cc4ff2-13e2-46ed-8fde-3bc8b6e29a0f/GCF_014197855.1_ASM1419785v1_genomic.fna.gz --refList GCF_014197855.1_ASM1419785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197855.1_ASM1419785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:04,681] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:04,691] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:04,692] [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_014197855.1	s__Rhodospira marina	100.0	1509	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	conclusive
GCF_009601025.1	s__Rhodospira navarrensis	81.8307	812	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	80.5157	761	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101965.1	s__Rhodospira trueperi	80.3761	655	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	79.668	638	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.5618	217	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	76.3572	144	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.2562	164	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	76.1817	161	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296935.1	s__Reyranella sp004296935	76.0282	163	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355005.1	s__Paracraurococcus ruber_A	75.7786	251	1510	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 10:51:04,693] [INFO] GTDB search result was written to GCF_014197855.1_ASM1419785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:04,694] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:04,697] [INFO] DFAST_QC result json was written to GCF_014197855.1_ASM1419785v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:04,697] [INFO] DFAST_QC completed!
[2024-01-24 10:51:04,698] [INFO] Total running time: 0h1m30s