[2024-01-24 12:21:44,725] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg6910d795-74ae-41de-9b18-28be5ea6398f/dqc_reference
[2024-01-24 12:21:46,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:46,020] [INFO] Task started: Prodigal
[2024-01-24 12:21:46,020] [INFO] Running command: gunzip -c /var/lib/cwl/stg47c5eff0-b0e4-4ad5-9797-5d70cbab82fd/GCF_014203135.1_ASM1420313v1_genomic.fna.gz | prodigal -d GCF_014203135.1_ASM1420313v1_genomic.fna/cds.fna -a GCF_014203135.1_ASM1420313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:00,145] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:00,145] [INFO] Task started: HMMsearch
[2024-01-24 12:22:00,145] [INFO] Running command: hmmsearch --tblout GCF_014203135.1_ASM1420313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6910d795-74ae-41de-9b18-28be5ea6398f/dqc_reference/reference_markers.hmm GCF_014203135.1_ASM1420313v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:00,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:00,482] [INFO] Found 6/6 markers.
[2024-01-24 12:22:00,552] [INFO] Query marker FASTA was written to GCF_014203135.1_ASM1420313v1_genomic.fna/markers.fasta
[2024-01-24 12:22:00,552] [INFO] Task started: Blastn
[2024-01-24 12:22:00,552] [INFO] Running command: blastn -query GCF_014203135.1_ASM1420313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6910d795-74ae-41de-9b18-28be5ea6398f/dqc_reference/reference_markers.fasta -out GCF_014203135.1_ASM1420313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:01,469] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:01,473] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:01,473] [INFO] Target genome list was writen to GCF_014203135.1_ASM1420313v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:01,478] [INFO] Task started: fastANI
[2024-01-24 12:22:01,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg47c5eff0-b0e4-4ad5-9797-5d70cbab82fd/GCF_014203135.1_ASM1420313v1_genomic.fna.gz --refList GCF_014203135.1_ASM1420313v1_genomic.fna/target_genomes.txt --output GCF_014203135.1_ASM1420313v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:18,391] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:18,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6910d795-74ae-41de-9b18-28be5ea6398f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:18,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6910d795-74ae-41de-9b18-28be5ea6398f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:18,406] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:22:18,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:18,407] [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_014203135.1	140057	140057	type	True	100.0	1507	1507	95	conclusive
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	99.9984	1505	1507	95	conclusive
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	99.9949	1487	1507	95	conclusive
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	81.8567	815	1507	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	80.6797	739	1507	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.8624	323	1507	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.6022	149	1507	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.5568	205	1507	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.4428	244	1507	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.3485	211	1507	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.2358	174	1507	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.1111	211	1507	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.1032	156	1507	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	76.0884	89	1507	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	76.0182	102	1507	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.0075	237	1507	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.8472	251	1507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:18,409] [INFO] DFAST Taxonomy check result was written to GCF_014203135.1_ASM1420313v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:18,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:18,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:18,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6910d795-74ae-41de-9b18-28be5ea6398f/dqc_reference/checkm_data
[2024-01-24 12:22:18,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:18,460] [INFO] Task started: CheckM
[2024-01-24 12:22:18,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203135.1_ASM1420313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203135.1_ASM1420313v1_genomic.fna/checkm_input GCF_014203135.1_ASM1420313v1_genomic.fna/checkm_result
[2024-01-24 12:23:06,398] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:06,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:06,426] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:06,426] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:06,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203135.1_ASM1420313v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:06,427] [INFO] Task started: Blastn
[2024-01-24 12:23:06,427] [INFO] Running command: blastn -query GCF_014203135.1_ASM1420313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6910d795-74ae-41de-9b18-28be5ea6398f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203135.1_ASM1420313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:07,899] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:07,902] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:07,903] [INFO] Target genome list was writen to GCF_014203135.1_ASM1420313v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:07,911] [INFO] Task started: fastANI
[2024-01-24 12:23:07,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg47c5eff0-b0e4-4ad5-9797-5d70cbab82fd/GCF_014203135.1_ASM1420313v1_genomic.fna.gz --refList GCF_014203135.1_ASM1420313v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203135.1_ASM1420313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:18,012] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:18,032] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:18,032] [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	99.9984	1505	1507	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	81.8439	818	1507	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	80.6611	742	1507	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	80.3786	653	1507	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	79.6916	627	1507	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	76.5669	205	1507	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	76.3627	142	1507	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	76.2974	161	1507	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	76.2427	149	1507	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	76.1207	155	1507	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	75.737	248	1507	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 12:23:18,034] [INFO] GTDB search result was written to GCF_014203135.1_ASM1420313v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:18,038] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:18,041] [INFO] DFAST_QC result json was written to GCF_014203135.1_ASM1420313v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:18,042] [INFO] DFAST_QC completed!
[2024-01-24 12:23:18,042] [INFO] Total running time: 0h1m33s