[2024-01-24 12:21:44,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,420] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaf1376f-b97e-4213-96ec-83c0fe9c842d/dqc_reference
[2024-01-24 12:21:45,974] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,975] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,975] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc8af4ed-4f88-4d03-96ac-099f79ac47a5/GCF_000022085.1_ASM2208v1_genomic.fna.gz | prodigal -d GCF_000022085.1_ASM2208v1_genomic.fna/cds.fna -a GCF_000022085.1_ASM2208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:11,387] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:11,387] [INFO] Task started: HMMsearch
[2024-01-24 12:22:11,387] [INFO] Running command: hmmsearch --tblout GCF_000022085.1_ASM2208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaf1376f-b97e-4213-96ec-83c0fe9c842d/dqc_reference/reference_markers.hmm GCF_000022085.1_ASM2208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:11,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:11,850] [INFO] Found 6/6 markers.
[2024-01-24 12:22:11,925] [INFO] Query marker FASTA was written to GCF_000022085.1_ASM2208v1_genomic.fna/markers.fasta
[2024-01-24 12:22:11,926] [INFO] Task started: Blastn
[2024-01-24 12:22:11,926] [INFO] Running command: blastn -query GCF_000022085.1_ASM2208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaf1376f-b97e-4213-96ec-83c0fe9c842d/dqc_reference/reference_markers.fasta -out GCF_000022085.1_ASM2208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:12,994] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:13,004] [INFO] Selected 20 target genomes.
[2024-01-24 12:22:13,005] [INFO] Target genome list was writen to GCF_000022085.1_ASM2208v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:13,012] [INFO] Task started: fastANI
[2024-01-24 12:22:13,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc8af4ed-4f88-4d03-96ac-099f79ac47a5/GCF_000022085.1_ASM2208v1_genomic.fna.gz --refList GCF_000022085.1_ASM2208v1_genomic.fna/target_genomes.txt --output GCF_000022085.1_ASM2208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:49,121] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:49,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaf1376f-b97e-4213-96ec-83c0fe9c842d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:49,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaf1376f-b97e-4213-96ec-83c0fe9c842d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:49,141] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:49,141] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:49,142] [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 nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	100.0	2938	2942	95	conclusive
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	84.5281	1354	2942	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	82.9703	1229	2942	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	82.9635	1238	2942	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	82.8988	1327	2942	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	82.8464	1315	2942	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	82.8402	1166	2942	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	82.8271	1324	2942	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	82.8242	1255	2942	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	82.8121	1142	2942	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	82.6379	1208	2942	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	82.5541	1294	2942	95	below_threshold
Methylobacterium aquaticum	strain=DSM 16371	GCA_001043915.1	270351	270351	type	True	82.3585	1161	2942	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	78.0323	411	2942	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.9982	426	2942	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	76.9364	273	2942	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	76.7101	359	2942	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	76.6718	309	2942	95	below_threshold
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	76.6497	264	2942	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	76.2463	223	2942	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:49,144] [INFO] DFAST Taxonomy check result was written to GCF_000022085.1_ASM2208v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:49,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:49,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:49,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaf1376f-b97e-4213-96ec-83c0fe9c842d/dqc_reference/checkm_data
[2024-01-24 12:22:49,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:49,233] [INFO] Task started: CheckM
[2024-01-24 12:22:49,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000022085.1_ASM2208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000022085.1_ASM2208v1_genomic.fna/checkm_input GCF_000022085.1_ASM2208v1_genomic.fna/checkm_result
[2024-01-24 12:24:11,603] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:11,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:11,630] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:11,631] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:11,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000022085.1_ASM2208v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:11,632] [INFO] Task started: Blastn
[2024-01-24 12:24:11,632] [INFO] Running command: blastn -query GCF_000022085.1_ASM2208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaf1376f-b97e-4213-96ec-83c0fe9c842d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000022085.1_ASM2208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:13,401] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:13,406] [INFO] Selected 20 target genomes.
[2024-01-24 12:24:13,406] [INFO] Target genome list was writen to GCF_000022085.1_ASM2208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:13,419] [INFO] Task started: fastANI
[2024-01-24 12:24:13,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc8af4ed-4f88-4d03-96ac-099f79ac47a5/GCF_000022085.1_ASM2208v1_genomic.fna.gz --refList GCF_000022085.1_ASM2208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000022085.1_ASM2208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:45,947] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:45,961] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:45,962] [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_000022085.1	s__Methylobacterium nodulans	100.0	2938	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000019365.1	s__Methylobacterium sp000019365	85.3113	1589	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
GCF_003173755.1	s__Methylobacterium terrae	82.9497	1243	2942	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	82.9235	1236	2942	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	82.9128	1250	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_001043975.1	s__Methylobacterium variabile	82.8885	1159	2942	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	82.8475	1321	2942	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	82.8296	1245	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058325.1	s__Methylobacterium currus	82.8199	1318	2942	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	82.6679	1267	2942	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	82.6639	1205	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151805.1	s__Methylobacterium sp006151805	82.5363	1298	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043915.1	s__Methylobacterium aquaticum	82.378	1159	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	78.0242	412	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966715.1	s__Blastochloris tepida	77.9316	434	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017487405.1	s__Brevundimonas sp017487405	76.2947	222	2942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312895.1	s__Luteimonas sp008312895	75.6071	199	2942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819515.1	s__Fen-999 sp018819515	75.4251	73	2942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:45,963] [INFO] GTDB search result was written to GCF_000022085.1_ASM2208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:45,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:45,968] [INFO] DFAST_QC result json was written to GCF_000022085.1_ASM2208v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:45,968] [INFO] DFAST_QC completed!
[2024-01-24 12:24:45,968] [INFO] Total running time: 0h3m2s