[2024-01-24 12:31:20,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:20,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:20,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg48a41ef9-b213-48f1-95c1-3985b955f99a/dqc_reference
[2024-01-24 12:31:21,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:21,735] [INFO] Task started: Prodigal
[2024-01-24 12:31:21,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a7f24fb-4c63-4db0-9e2f-7955baaf4147/GCF_003173735.1_ASM317373v1_genomic.fna.gz | prodigal -d GCF_003173735.1_ASM317373v1_genomic.fna/cds.fna -a GCF_003173735.1_ASM317373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:36,294] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:36,294] [INFO] Task started: HMMsearch
[2024-01-24 12:31:36,294] [INFO] Running command: hmmsearch --tblout GCF_003173735.1_ASM317373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48a41ef9-b213-48f1-95c1-3985b955f99a/dqc_reference/reference_markers.hmm GCF_003173735.1_ASM317373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:36,552] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:36,553] [INFO] Found 6/6 markers.
[2024-01-24 12:31:36,598] [INFO] Query marker FASTA was written to GCF_003173735.1_ASM317373v1_genomic.fna/markers.fasta
[2024-01-24 12:31:36,598] [INFO] Task started: Blastn
[2024-01-24 12:31:36,598] [INFO] Running command: blastn -query GCF_003173735.1_ASM317373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48a41ef9-b213-48f1-95c1-3985b955f99a/dqc_reference/reference_markers.fasta -out GCF_003173735.1_ASM317373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:37,570] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:37,574] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:37,575] [INFO] Target genome list was writen to GCF_003173735.1_ASM317373v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:37,580] [INFO] Task started: fastANI
[2024-01-24 12:31:37,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a7f24fb-4c63-4db0-9e2f-7955baaf4147/GCF_003173735.1_ASM317373v1_genomic.fna.gz --refList GCF_003173735.1_ASM317373v1_genomic.fna/target_genomes.txt --output GCF_003173735.1_ASM317373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:53,817] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:53,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48a41ef9-b213-48f1-95c1-3985b955f99a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:53,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48a41ef9-b213-48f1-95c1-3985b955f99a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:53,827] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:53,827] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:53,827] [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 radiodurans	strain=17Sr1-43	GCA_003173735.1	2202828	2202828	type	True	100.0	1844	1846	95	conclusive
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	90.8246	1377	1846	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	90.5306	1313	1846	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	86.3449	1184	1846	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	86.3394	1247	1846	95	below_threshold
Methylobacterium symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	85.7045	1178	1846	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	83.6662	1023	1846	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	82.559	1093	1846	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	82.2007	1058	1846	95	below_threshold
Bradyrhizobium archetypum	strain=WSM 1744	GCA_013114835.1	2721160	2721160	type	True	76.9617	304	1846	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	76.0029	313	1846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:53,829] [INFO] DFAST Taxonomy check result was written to GCF_003173735.1_ASM317373v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:53,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:53,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:53,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48a41ef9-b213-48f1-95c1-3985b955f99a/dqc_reference/checkm_data
[2024-01-24 12:31:53,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:53,881] [INFO] Task started: CheckM
[2024-01-24 12:31:53,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003173735.1_ASM317373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003173735.1_ASM317373v1_genomic.fna/checkm_input GCF_003173735.1_ASM317373v1_genomic.fna/checkm_result
[2024-01-24 12:32:36,987] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:36,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:37,008] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:37,008] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:37,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003173735.1_ASM317373v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:37,009] [INFO] Task started: Blastn
[2024-01-24 12:32:37,009] [INFO] Running command: blastn -query GCF_003173735.1_ASM317373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48a41ef9-b213-48f1-95c1-3985b955f99a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003173735.1_ASM317373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:38,778] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:38,781] [INFO] Selected 17 target genomes.
[2024-01-24 12:32:38,781] [INFO] Target genome list was writen to GCF_003173735.1_ASM317373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:38,802] [INFO] Task started: fastANI
[2024-01-24 12:32:38,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a7f24fb-4c63-4db0-9e2f-7955baaf4147/GCF_003173735.1_ASM317373v1_genomic.fna.gz --refList GCF_003173735.1_ASM317373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003173735.1_ASM317373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:03,199] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:03,213] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:03,213] [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_003173735.1	s__Methylobacterium radiodurans	100.0	1845	1846	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_902141855.1	s__Methylobacterium dankookense	86.3692	1244	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141845.1	s__Methylobacterium symbioticum	85.7274	1175	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992195.1	s__Methylobacterium oxalidis	83.5429	1030	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	83.3322	1061	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_008806345.1	s__Methylobacterium sp008806345	83.2311	1084	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003096615.1	s__Methylobacterium organophilum	83.1024	1130	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
GCF_900112625.1	s__Methylobacterium sp900112625	82.9669	1126	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_009806555.1	s__Methylobacterium sp009806555	82.7285	1099	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364445.2	s__Methylobacterium mesophilicum	82.641	1068	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201865.1	s__Methylobacterium sp003201865	82.6252	996	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697185.1	s__Methylobacterium brachiatum	82.535	1075	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.08	95.77	0.85	0.80	4	-
GCF_900114535.1	s__Methylobacterium pseudosasicola	82.3654	1048	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138435.1	s__Methylobacterium fujisawaense	82.3443	1063	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	-
GCF_001043955.1	s__Methylobacterium tarhaniae	81.323	941	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019365.1	s__Methylobacterium sp000019365	81.1548	1020	1846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
GCF_001854325.1	s__Cupriavidus malaysiensis	75.469	319	1846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.34	99.30	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:03,214] [INFO] GTDB search result was written to GCF_003173735.1_ASM317373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:03,215] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:03,218] [INFO] DFAST_QC result json was written to GCF_003173735.1_ASM317373v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:03,219] [INFO] DFAST_QC completed!
[2024-01-24 12:33:03,219] [INFO] Total running time: 0h1m43s