[2024-01-24 13:36:58,369] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:58,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:58,371] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3e4acae-fb99-4b28-bd02-7b7c55758008/dqc_reference
[2024-01-24 13:36:59,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:59,559] [INFO] Task started: Prodigal
[2024-01-24 13:36:59,559] [INFO] Running command: gunzip -c /var/lib/cwl/stgaba78c60-36f8-4f89-918b-4995042711fe/GCF_014138435.1_ASM1413843v1_genomic.fna.gz | prodigal -d GCF_014138435.1_ASM1413843v1_genomic.fna/cds.fna -a GCF_014138435.1_ASM1413843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:15,339] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:15,339] [INFO] Task started: HMMsearch
[2024-01-24 13:37:15,339] [INFO] Running command: hmmsearch --tblout GCF_014138435.1_ASM1413843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3e4acae-fb99-4b28-bd02-7b7c55758008/dqc_reference/reference_markers.hmm GCF_014138435.1_ASM1413843v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:15,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:15,765] [INFO] Found 6/6 markers.
[2024-01-24 13:37:15,830] [INFO] Query marker FASTA was written to GCF_014138435.1_ASM1413843v1_genomic.fna/markers.fasta
[2024-01-24 13:37:15,830] [INFO] Task started: Blastn
[2024-01-24 13:37:15,830] [INFO] Running command: blastn -query GCF_014138435.1_ASM1413843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3e4acae-fb99-4b28-bd02-7b7c55758008/dqc_reference/reference_markers.fasta -out GCF_014138435.1_ASM1413843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:16,816] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:16,820] [INFO] Selected 11 target genomes.
[2024-01-24 13:37:16,821] [INFO] Target genome list was writen to GCF_014138435.1_ASM1413843v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:16,828] [INFO] Task started: fastANI
[2024-01-24 13:37:16,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgaba78c60-36f8-4f89-918b-4995042711fe/GCF_014138435.1_ASM1413843v1_genomic.fna.gz --refList GCF_014138435.1_ASM1413843v1_genomic.fna/target_genomes.txt --output GCF_014138435.1_ASM1413843v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:34,413] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:34,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3e4acae-fb99-4b28-bd02-7b7c55758008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:34,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3e4acae-fb99-4b28-bd02-7b7c55758008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:34,424] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:34,424] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:34,424] [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 phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	98.8469	1829	1980	95	conclusive
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	98.8211	1806	1980	95	conclusive
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	90.8188	1630	1980	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	90.7727	1587	1980	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	88.2673	1459	1980	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	88.218	1487	1980	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	87.278	1402	1980	95	below_threshold
Methylobacterium phyllostachyos	strain=BL47	GCA_900103445.1	582672	582672	type	True	86.7875	1375	1980	95	below_threshold
Methylobacterium pseudosasicola	strain=BL36	GCA_900114535.1	582667	582667	type	True	85.8144	1401	1980	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	85.7145	1362	1980	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	82.6571	1035	1980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:34,426] [INFO] DFAST Taxonomy check result was written to GCF_014138435.1_ASM1413843v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:34,426] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:34,426] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:34,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3e4acae-fb99-4b28-bd02-7b7c55758008/dqc_reference/checkm_data
[2024-01-24 13:37:34,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:34,484] [INFO] Task started: CheckM
[2024-01-24 13:37:34,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138435.1_ASM1413843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138435.1_ASM1413843v1_genomic.fna/checkm_input GCF_014138435.1_ASM1413843v1_genomic.fna/checkm_result
[2024-01-24 13:38:26,297] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:26,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:26,321] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:26,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:26,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138435.1_ASM1413843v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:26,322] [INFO] Task started: Blastn
[2024-01-24 13:38:26,322] [INFO] Running command: blastn -query GCF_014138435.1_ASM1413843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3e4acae-fb99-4b28-bd02-7b7c55758008/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138435.1_ASM1413843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:28,160] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:28,163] [INFO] Selected 11 target genomes.
[2024-01-24 13:38:28,163] [INFO] Target genome list was writen to GCF_014138435.1_ASM1413843v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:28,176] [INFO] Task started: fastANI
[2024-01-24 13:38:28,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgaba78c60-36f8-4f89-918b-4995042711fe/GCF_014138435.1_ASM1413843v1_genomic.fna.gz --refList GCF_014138435.1_ASM1413843v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138435.1_ASM1413843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:45,964] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:45,974] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:45,975] [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_014138435.1	s__Methylobacterium fujisawaense	100.0	1978	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	conclusive
GCA_003096615.1	s__Methylobacterium organophilum	90.8493	1632	1980	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	90.7504	1588	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_900103195.1	s__Methylobacterium sp900103195	90.2624	1560	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_014873335.1	s__Methylobacterium sp014873335	87.9131	1460	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017833295.1	s__Methylobacterium sp017833295	87.4963	1481	1980	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	87.4274	1435	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009806555.1	s__Methylobacterium sp009806555	87.3585	1402	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103445.1	s__Methylobacterium phyllostachyos	86.7745	1376	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173735.1	s__Methylobacterium radiodurans	82.4061	1049	1980	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	80.0373	986	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:45,977] [INFO] GTDB search result was written to GCF_014138435.1_ASM1413843v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:45,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:45,982] [INFO] DFAST_QC result json was written to GCF_014138435.1_ASM1413843v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:45,982] [INFO] DFAST_QC completed!
[2024-01-24 13:38:45,982] [INFO] Total running time: 0h1m48s