[2024-01-25 17:58:50,586] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:50,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:50,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ac86717-4b41-477c-a30b-f31d36aac012/dqc_reference
[2024-01-25 17:58:51,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:51,728] [INFO] Task started: Prodigal
[2024-01-25 17:58:51,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d64f97b-9471-4523-a31b-54462e4b57ad/GCF_014199935.1_ASM1419993v1_genomic.fna.gz | prodigal -d GCF_014199935.1_ASM1419993v1_genomic.fna/cds.fna -a GCF_014199935.1_ASM1419993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:59:04,254] [INFO] Task succeeded: Prodigal
[2024-01-25 17:59:04,254] [INFO] Task started: HMMsearch
[2024-01-25 17:59:04,254] [INFO] Running command: hmmsearch --tblout GCF_014199935.1_ASM1419993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ac86717-4b41-477c-a30b-f31d36aac012/dqc_reference/reference_markers.hmm GCF_014199935.1_ASM1419993v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:59:04,539] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:59:04,540] [INFO] Found 6/6 markers.
[2024-01-25 17:59:04,581] [INFO] Query marker FASTA was written to GCF_014199935.1_ASM1419993v1_genomic.fna/markers.fasta
[2024-01-25 17:59:04,581] [INFO] Task started: Blastn
[2024-01-25 17:59:04,581] [INFO] Running command: blastn -query GCF_014199935.1_ASM1419993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ac86717-4b41-477c-a30b-f31d36aac012/dqc_reference/reference_markers.fasta -out GCF_014199935.1_ASM1419993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:05,571] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:05,574] [INFO] Selected 10 target genomes.
[2024-01-25 17:59:05,574] [INFO] Target genome list was writen to GCF_014199935.1_ASM1419993v1_genomic.fna/target_genomes.txt
[2024-01-25 17:59:05,584] [INFO] Task started: fastANI
[2024-01-25 17:59:05,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d64f97b-9471-4523-a31b-54462e4b57ad/GCF_014199935.1_ASM1419993v1_genomic.fna.gz --refList GCF_014199935.1_ASM1419993v1_genomic.fna/target_genomes.txt --output GCF_014199935.1_ASM1419993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:20,965] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:20,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ac86717-4b41-477c-a30b-f31d36aac012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:20,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ac86717-4b41-477c-a30b-f31d36aac012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:20,976] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:59:20,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:59:20,976] [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
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	100.0	1772	1774	95	conclusive
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	90.5165	1342	1774	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	87.4091	1294	1774	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	86.3416	918	1774	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	85.4361	1204	1774	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	85.4227	1205	1774	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	85.3485	1198	1774	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	85.2713	1022	1774	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	82.9514	1055	1774	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.7267	781	1774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:20,978] [INFO] DFAST Taxonomy check result was written to GCF_014199935.1_ASM1419993v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:20,978] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:20,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:20,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ac86717-4b41-477c-a30b-f31d36aac012/dqc_reference/checkm_data
[2024-01-25 17:59:20,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:21,031] [INFO] Task started: CheckM
[2024-01-25 17:59:21,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199935.1_ASM1419993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199935.1_ASM1419993v1_genomic.fna/checkm_input GCF_014199935.1_ASM1419993v1_genomic.fna/checkm_result
[2024-01-25 18:00:01,877] [INFO] Task succeeded: CheckM
[2024-01-25 18:00:01,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:00:01,897] [INFO] ===== Completeness check finished =====
[2024-01-25 18:00:01,898] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:00:01,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199935.1_ASM1419993v1_genomic.fna/markers.fasta)
[2024-01-25 18:00:01,901] [INFO] Task started: Blastn
[2024-01-25 18:00:01,901] [INFO] Running command: blastn -query GCF_014199935.1_ASM1419993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ac86717-4b41-477c-a30b-f31d36aac012/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199935.1_ASM1419993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:03,954] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:03,956] [INFO] Selected 9 target genomes.
[2024-01-25 18:00:03,957] [INFO] Target genome list was writen to GCF_014199935.1_ASM1419993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:00:03,973] [INFO] Task started: fastANI
[2024-01-25 18:00:03,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d64f97b-9471-4523-a31b-54462e4b57ad/GCF_014199935.1_ASM1419993v1_genomic.fna.gz --refList GCF_014199935.1_ASM1419993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199935.1_ASM1419993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:00:18,745] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:18,752] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:00:18,752] [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_014199935.1	s__Methylobacterium rhodinum	100.0	1772	1774	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_001425465.1	s__Methylobacterium sp001425465	91.088	1391	1774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114375.1	s__Methylobacterium salsuginis	90.5263	1340	1774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502455.1	s__Methylobacterium sp005502455	87.3958	1236	1774	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	85.7	1196	1774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355515.1	s__Methylobacterium populi_A	85.566	1228	1774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900234795.1	s__Methylobacterium extorquens	85.3921	1209	1774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	-
GCF_001542815.1	s__Methylobacterium sp001542815	85.3069	1202	1774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.78	0.92	0.92	2	-
GCF_014845115.1	s__Methylobacterium zatmanii	85.2635	1022	1774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:00:18,753] [INFO] GTDB search result was written to GCF_014199935.1_ASM1419993v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:00:18,754] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:00:18,756] [INFO] DFAST_QC result json was written to GCF_014199935.1_ASM1419993v1_genomic.fna/dqc_result.json
[2024-01-25 18:00:18,756] [INFO] DFAST_QC completed!
[2024-01-25 18:00:18,756] [INFO] Total running time: 0h1m28s