[2024-01-24 13:13:46,499] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:46,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:46,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg43fee9d5-5e68-4c0b-8a78-683549382119/dqc_reference
[2024-01-24 13:13:47,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:47,775] [INFO] Task started: Prodigal
[2024-01-24 13:13:47,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a0db98f-a636-4c79-8c34-f2af7910aaf9/GCF_030815195.1_ASM3081519v1_genomic.fna.gz | prodigal -d GCF_030815195.1_ASM3081519v1_genomic.fna/cds.fna -a GCF_030815195.1_ASM3081519v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:05,767] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:05,767] [INFO] Task started: HMMsearch
[2024-01-24 13:14:05,768] [INFO] Running command: hmmsearch --tblout GCF_030815195.1_ASM3081519v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43fee9d5-5e68-4c0b-8a78-683549382119/dqc_reference/reference_markers.hmm GCF_030815195.1_ASM3081519v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:06,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:06,079] [INFO] Found 6/6 markers.
[2024-01-24 13:14:06,138] [INFO] Query marker FASTA was written to GCF_030815195.1_ASM3081519v1_genomic.fna/markers.fasta
[2024-01-24 13:14:06,138] [INFO] Task started: Blastn
[2024-01-24 13:14:06,138] [INFO] Running command: blastn -query GCF_030815195.1_ASM3081519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43fee9d5-5e68-4c0b-8a78-683549382119/dqc_reference/reference_markers.fasta -out GCF_030815195.1_ASM3081519v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:07,098] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:07,102] [INFO] Selected 11 target genomes.
[2024-01-24 13:14:07,103] [INFO] Target genome list was writen to GCF_030815195.1_ASM3081519v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:07,106] [INFO] Task started: fastANI
[2024-01-24 13:14:07,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a0db98f-a636-4c79-8c34-f2af7910aaf9/GCF_030815195.1_ASM3081519v1_genomic.fna.gz --refList GCF_030815195.1_ASM3081519v1_genomic.fna/target_genomes.txt --output GCF_030815195.1_ASM3081519v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:25,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:25,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43fee9d5-5e68-4c0b-8a78-683549382119/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:25,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43fee9d5-5e68-4c0b-8a78-683549382119/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:25,708] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:25,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:25,708] [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 brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	99.998	2166	2233	95	conclusive
Methylobacterium pseudosasicola	strain=BL36	GCA_900114535.1	582667	582667	type	True	91.2725	1569	2233	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	90.4269	1560	2233	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	86.4026	1413	2233	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	86.3666	1437	2233	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	86.3011	1421	2233	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	86.2529	1469	2233	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	85.8805	1423	2233	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	85.8462	1410	2233	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	85.6104	1374	2233	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	82.5537	1052	2233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:25,710] [INFO] DFAST Taxonomy check result was written to GCF_030815195.1_ASM3081519v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:25,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:25,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:25,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43fee9d5-5e68-4c0b-8a78-683549382119/dqc_reference/checkm_data
[2024-01-24 13:14:25,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:25,774] [INFO] Task started: CheckM
[2024-01-24 13:14:25,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030815195.1_ASM3081519v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030815195.1_ASM3081519v1_genomic.fna/checkm_input GCF_030815195.1_ASM3081519v1_genomic.fna/checkm_result
[2024-01-24 13:15:19,061] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:19,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:19,090] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:19,090] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:19,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030815195.1_ASM3081519v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:19,091] [INFO] Task started: Blastn
[2024-01-24 13:15:19,091] [INFO] Running command: blastn -query GCF_030815195.1_ASM3081519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43fee9d5-5e68-4c0b-8a78-683549382119/dqc_reference/reference_markers_gtdb.fasta -out GCF_030815195.1_ASM3081519v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:20,866] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:20,870] [INFO] Selected 5 target genomes.
[2024-01-24 13:15:20,870] [INFO] Target genome list was writen to GCF_030815195.1_ASM3081519v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:20,875] [INFO] Task started: fastANI
[2024-01-24 13:15:20,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a0db98f-a636-4c79-8c34-f2af7910aaf9/GCF_030815195.1_ASM3081519v1_genomic.fna.gz --refList GCF_030815195.1_ASM3081519v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030815195.1_ASM3081519v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:30,889] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:30,900] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:30,900] [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_003697185.1	s__Methylobacterium brachiatum	97.5822	1804	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.08	95.77	0.85	0.80	4	conclusive
GCF_900114535.1	s__Methylobacterium pseudosasicola	91.3178	1565	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001455965.1	s__Methylobacterium sp001455965	90.4546	1535	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040085.1	s__Methylobacterium sp008040085	90.3841	1470	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000895.1	s__Methylobacterium sp008000895	89.9069	1577	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	98.22	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:30,902] [INFO] GTDB search result was written to GCF_030815195.1_ASM3081519v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:30,903] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:30,906] [INFO] DFAST_QC result json was written to GCF_030815195.1_ASM3081519v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:30,906] [INFO] DFAST_QC completed!
[2024-01-24 13:15:30,906] [INFO] Total running time: 0h1m44s