[2024-01-25 18:52:05,707] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:05,708] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:05,708] [INFO] DQC Reference Directory: /var/lib/cwl/stgd16d5ab5-1548-4fe0-b06d-ab99982ab5a3/dqc_reference
[2024-01-25 18:52:06,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:06,913] [INFO] Task started: Prodigal
[2024-01-25 18:52:06,913] [INFO] Running command: gunzip -c /var/lib/cwl/stgaaf5fd2b-3e85-4c6e-a147-7ea654483bb3/GCF_026344005.1_ASM2634400v1_genomic.fna.gz | prodigal -d GCF_026344005.1_ASM2634400v1_genomic.fna/cds.fna -a GCF_026344005.1_ASM2634400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:21,084] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:21,085] [INFO] Task started: HMMsearch
[2024-01-25 18:52:21,085] [INFO] Running command: hmmsearch --tblout GCF_026344005.1_ASM2634400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd16d5ab5-1548-4fe0-b06d-ab99982ab5a3/dqc_reference/reference_markers.hmm GCF_026344005.1_ASM2634400v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:21,396] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:21,397] [INFO] Found 6/6 markers.
[2024-01-25 18:52:21,441] [INFO] Query marker FASTA was written to GCF_026344005.1_ASM2634400v1_genomic.fna/markers.fasta
[2024-01-25 18:52:21,441] [INFO] Task started: Blastn
[2024-01-25 18:52:21,442] [INFO] Running command: blastn -query GCF_026344005.1_ASM2634400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd16d5ab5-1548-4fe0-b06d-ab99982ab5a3/dqc_reference/reference_markers.fasta -out GCF_026344005.1_ASM2634400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:22,421] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:22,425] [INFO] Selected 16 target genomes.
[2024-01-25 18:52:22,425] [INFO] Target genome list was writen to GCF_026344005.1_ASM2634400v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:22,431] [INFO] Task started: fastANI
[2024-01-25 18:52:22,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaf5fd2b-3e85-4c6e-a147-7ea654483bb3/GCF_026344005.1_ASM2634400v1_genomic.fna.gz --refList GCF_026344005.1_ASM2634400v1_genomic.fna/target_genomes.txt --output GCF_026344005.1_ASM2634400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:40,764] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:40,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd16d5ab5-1548-4fe0-b06d-ab99982ab5a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:40,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd16d5ab5-1548-4fe0-b06d-ab99982ab5a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:40,775] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:52:40,775] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:52:40,775] [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 granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	85.7797	1238	1849	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	85.0126	1185	1849	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	80.3898	834	1849	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	79.8494	732	1849	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	77.8661	359	1849	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.6472	406	1849	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	77.5632	401	1849	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	77.5069	284	1849	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	77.4873	434	1849	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	77.4725	392	1849	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.2308	245	1849	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	77.1642	297	1849	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.1461	336	1849	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.1428	336	1849	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.9316	342	1849	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.7426	351	1849	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:40,777] [INFO] DFAST Taxonomy check result was written to GCF_026344005.1_ASM2634400v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:40,777] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:40,777] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:40,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd16d5ab5-1548-4fe0-b06d-ab99982ab5a3/dqc_reference/checkm_data
[2024-01-25 18:52:40,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:40,830] [INFO] Task started: CheckM
[2024-01-25 18:52:40,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026344005.1_ASM2634400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026344005.1_ASM2634400v1_genomic.fna/checkm_input GCF_026344005.1_ASM2634400v1_genomic.fna/checkm_result
[2024-01-25 18:53:22,696] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:22,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:22,747] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:22,747] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:22,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026344005.1_ASM2634400v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:22,748] [INFO] Task started: Blastn
[2024-01-25 18:53:22,748] [INFO] Running command: blastn -query GCF_026344005.1_ASM2634400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd16d5ab5-1548-4fe0-b06d-ab99982ab5a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_026344005.1_ASM2634400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:24,825] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:24,833] [INFO] Selected 8 target genomes.
[2024-01-25 18:53:24,833] [INFO] Target genome list was writen to GCF_026344005.1_ASM2634400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:24,839] [INFO] Task started: fastANI
[2024-01-25 18:53:24,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaf5fd2b-3e85-4c6e-a147-7ea654483bb3/GCF_026344005.1_ASM2634400v1_genomic.fna.gz --refList GCF_026344005.1_ASM2634400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026344005.1_ASM2634400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:35,131] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:35,137] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:53:35,138] [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_017305815.1	s__Kaistia sp017305815	86.6185	844	1849	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	85.7797	1238	1849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	85.4761	1225	1849	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	85.0433	1182	1849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	80.4677	759	1849	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	80.4034	833	1849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_900129325.1	s__Kaistia soli	79.8563	731	1849	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	79.5617	622	1849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:35,139] [INFO] GTDB search result was written to GCF_026344005.1_ASM2634400v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:35,140] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:35,144] [INFO] DFAST_QC result json was written to GCF_026344005.1_ASM2634400v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:35,144] [INFO] DFAST_QC completed!
[2024-01-25 18:53:35,144] [INFO] Total running time: 0h1m29s