[2024-01-24 14:19:46,558] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e4fa083-4d6c-472c-9895-d017bbb1e602/dqc_reference
[2024-01-24 14:19:47,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,891] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg00e63180-706a-40d6-be98-a02c96b1af5a/GCF_030409475.1_ASM3040947v1_genomic.fna.gz | prodigal -d GCF_030409475.1_ASM3040947v1_genomic.fna/cds.fna -a GCF_030409475.1_ASM3040947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:06,286] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:06,287] [INFO] Task started: HMMsearch
[2024-01-24 14:20:06,287] [INFO] Running command: hmmsearch --tblout GCF_030409475.1_ASM3040947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e4fa083-4d6c-472c-9895-d017bbb1e602/dqc_reference/reference_markers.hmm GCF_030409475.1_ASM3040947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:06,630] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:06,631] [INFO] Found 6/6 markers.
[2024-01-24 14:20:06,688] [INFO] Query marker FASTA was written to GCF_030409475.1_ASM3040947v1_genomic.fna/markers.fasta
[2024-01-24 14:20:06,689] [INFO] Task started: Blastn
[2024-01-24 14:20:06,689] [INFO] Running command: blastn -query GCF_030409475.1_ASM3040947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e4fa083-4d6c-472c-9895-d017bbb1e602/dqc_reference/reference_markers.fasta -out GCF_030409475.1_ASM3040947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:07,894] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:07,900] [INFO] Selected 15 target genomes.
[2024-01-24 14:20:07,901] [INFO] Target genome list was writen to GCF_030409475.1_ASM3040947v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:07,932] [INFO] Task started: fastANI
[2024-01-24 14:20:07,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e63180-706a-40d6-be98-a02c96b1af5a/GCF_030409475.1_ASM3040947v1_genomic.fna.gz --refList GCF_030409475.1_ASM3040947v1_genomic.fna/target_genomes.txt --output GCF_030409475.1_ASM3040947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:35,935] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:35,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e4fa083-4d6c-472c-9895-d017bbb1e602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:35,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e4fa083-4d6c-472c-9895-d017bbb1e602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:35,949] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:35,949] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:35,949] [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
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	99.9624	2175	2254	95	conclusive
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	84.6098	1351	2254	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	84.057	1388	2254	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	83.96	1255	2254	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	83.9299	1340	2254	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	83.8066	1260	2254	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	83.7384	1241	2254	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	83.615	1165	2254	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	83.5423	1269	2254	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	83.4978	1163	2254	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	83.4643	1342	2254	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	83.4576	1324	2254	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	83.434	1188	2254	95	below_threshold
Methylobacterium frigidaeris	strain=IER25-16	GCA_002759055.1	2038277	2038277	type	True	83.2784	850	2254	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	83.2347	1286	2254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:35,951] [INFO] DFAST Taxonomy check result was written to GCF_030409475.1_ASM3040947v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:35,952] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:35,952] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:35,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e4fa083-4d6c-472c-9895-d017bbb1e602/dqc_reference/checkm_data
[2024-01-24 14:20:35,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:36,020] [INFO] Task started: CheckM
[2024-01-24 14:20:36,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409475.1_ASM3040947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409475.1_ASM3040947v1_genomic.fna/checkm_input GCF_030409475.1_ASM3040947v1_genomic.fna/checkm_result
[2024-01-24 14:21:34,527] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:34,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:34,548] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:34,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:34,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409475.1_ASM3040947v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:34,549] [INFO] Task started: Blastn
[2024-01-24 14:21:34,549] [INFO] Running command: blastn -query GCF_030409475.1_ASM3040947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e4fa083-4d6c-472c-9895-d017bbb1e602/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409475.1_ASM3040947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:36,642] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:36,645] [INFO] Selected 13 target genomes.
[2024-01-24 14:21:36,646] [INFO] Target genome list was writen to GCF_030409475.1_ASM3040947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:36,667] [INFO] Task started: fastANI
[2024-01-24 14:21:36,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e63180-706a-40d6-be98-a02c96b1af5a/GCF_030409475.1_ASM3040947v1_genomic.fna.gz --refList GCF_030409475.1_ASM3040947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409475.1_ASM3040947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:00,266] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:00,278] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:22:00,278] [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_000019365.1	s__Methylobacterium sp000019365	84.6594	1428	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
GCF_000022085.1	s__Methylobacterium nodulans	84.6342	1346	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745635.1	s__Methylobacterium sp004745635	84.0427	1389	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574465.1	s__Methylobacterium crusticola	83.9506	1257	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173755.1	s__Methylobacterium terrae	83.8216	1257	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004004555.2	s__Methylobacterium sp004004555	83.7284	1243	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173775.1	s__Methylobacterium sp003173775	83.5643	1277	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_003058325.1	s__Methylobacterium currus	83.5082	1334	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043955.1	s__Methylobacterium tarhaniae	83.4629	1184	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043735.1	s__Methylobacterium sp011043735	83.4026	1326	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016804325.1	s__Methylobacterium aquaticum_C	83.3387	1288	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002759055.1	s__Methylobacterium frigidaeris	83.2852	850	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019216885.1	s__Methylobacterium sp019216885	83.1548	1287	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:00,279] [INFO] GTDB search result was written to GCF_030409475.1_ASM3040947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:00,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:00,284] [INFO] DFAST_QC result json was written to GCF_030409475.1_ASM3040947v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:00,284] [INFO] DFAST_QC completed!
[2024-01-24 14:22:00,284] [INFO] Total running time: 0h2m14s