[2024-01-24 14:56:23,785] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg98e30564-2e13-46d2-9c2f-e9d3990bb93b/dqc_reference
[2024-01-24 14:56:26,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,556] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,556] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8286425-2a33-4327-9002-f5d2b9c8ad31/GCF_030815145.1_ASM3081514v1_genomic.fna.gz | prodigal -d GCF_030815145.1_ASM3081514v1_genomic.fna/cds.fna -a GCF_030815145.1_ASM3081514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:40,410] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:40,411] [INFO] Task started: HMMsearch
[2024-01-24 14:56:40,411] [INFO] Running command: hmmsearch --tblout GCF_030815145.1_ASM3081514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98e30564-2e13-46d2-9c2f-e9d3990bb93b/dqc_reference/reference_markers.hmm GCF_030815145.1_ASM3081514v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:40,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:40,753] [INFO] Found 6/6 markers.
[2024-01-24 14:56:40,811] [INFO] Query marker FASTA was written to GCF_030815145.1_ASM3081514v1_genomic.fna/markers.fasta
[2024-01-24 14:56:40,812] [INFO] Task started: Blastn
[2024-01-24 14:56:40,812] [INFO] Running command: blastn -query GCF_030815145.1_ASM3081514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98e30564-2e13-46d2-9c2f-e9d3990bb93b/dqc_reference/reference_markers.fasta -out GCF_030815145.1_ASM3081514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:41,919] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:41,923] [INFO] Selected 15 target genomes.
[2024-01-24 14:56:41,924] [INFO] Target genome list was writen to GCF_030815145.1_ASM3081514v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:41,931] [INFO] Task started: fastANI
[2024-01-24 14:56:41,932] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8286425-2a33-4327-9002-f5d2b9c8ad31/GCF_030815145.1_ASM3081514v1_genomic.fna.gz --refList GCF_030815145.1_ASM3081514v1_genomic.fna/target_genomes.txt --output GCF_030815145.1_ASM3081514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:58,764] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:58,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98e30564-2e13-46d2-9c2f-e9d3990bb93b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:58,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98e30564-2e13-46d2-9c2f-e9d3990bb93b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:58,778] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:56:58,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:56:58,778] [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
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	82.4441	1100	1529	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	82.0555	991	1529	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	81.5019	843	1529	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	81.0387	796	1529	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.2609	551	1529	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.109	497	1529	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	78.0033	473	1529	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.8507	449	1529	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	77.7859	446	1529	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	77.7161	327	1529	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.6291	408	1529	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.5966	480	1529	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.5509	356	1529	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.1359	296	1529	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.9454	476	1529	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:58,780] [INFO] DFAST Taxonomy check result was written to GCF_030815145.1_ASM3081514v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:58,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:58,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:58,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98e30564-2e13-46d2-9c2f-e9d3990bb93b/dqc_reference/checkm_data
[2024-01-24 14:56:58,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:58,826] [INFO] Task started: CheckM
[2024-01-24 14:56:58,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030815145.1_ASM3081514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030815145.1_ASM3081514v1_genomic.fna/checkm_input GCF_030815145.1_ASM3081514v1_genomic.fna/checkm_result
[2024-01-24 14:57:47,905] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:47,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:47,957] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:47,957] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:47,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030815145.1_ASM3081514v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:47,958] [INFO] Task started: Blastn
[2024-01-24 14:57:47,958] [INFO] Running command: blastn -query GCF_030815145.1_ASM3081514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98e30564-2e13-46d2-9c2f-e9d3990bb93b/dqc_reference/reference_markers_gtdb.fasta -out GCF_030815145.1_ASM3081514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:50,391] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:50,400] [INFO] Selected 8 target genomes.
[2024-01-24 14:57:50,400] [INFO] Target genome list was writen to GCF_030815145.1_ASM3081514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:50,409] [INFO] Task started: fastANI
[2024-01-24 14:57:50,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8286425-2a33-4327-9002-f5d2b9c8ad31/GCF_030815145.1_ASM3081514v1_genomic.fna.gz --refList GCF_030815145.1_ASM3081514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030815145.1_ASM3081514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:00,133] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:00,141] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:58:00,141] [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
GCA_017307955.1	s__Kaistia sp017307955	91.1674	1353	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129325.1	s__Kaistia soli	82.43	1100	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	82.002	999	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_016629525.1	s__Kaistia sp016629525	81.6505	835	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	81.4929	844	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305815.1	s__Kaistia sp017305815	81.0381	613	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380505.1	s__Kaistia granuli	80.9965	802	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	80.3421	756	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:00,143] [INFO] GTDB search result was written to GCF_030815145.1_ASM3081514v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:00,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:00,150] [INFO] DFAST_QC result json was written to GCF_030815145.1_ASM3081514v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:00,150] [INFO] DFAST_QC completed!
[2024-01-24 14:58:00,150] [INFO] Total running time: 0h1m36s