[2024-01-24 13:12:52,841] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:52,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:52,843] [INFO] DQC Reference Directory: /var/lib/cwl/stge250a15d-94c9-4c6c-8355-f429048083f1/dqc_reference
[2024-01-24 13:12:54,149] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:54,150] [INFO] Task started: Prodigal
[2024-01-24 13:12:54,150] [INFO] Running command: gunzip -c /var/lib/cwl/stge353ddc0-3484-4415-8e15-2c58ffd022fe/GCF_014196345.1_ASM1419634v1_genomic.fna.gz | prodigal -d GCF_014196345.1_ASM1419634v1_genomic.fna/cds.fna -a GCF_014196345.1_ASM1419634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:11,164] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:11,165] [INFO] Task started: HMMsearch
[2024-01-24 13:13:11,165] [INFO] Running command: hmmsearch --tblout GCF_014196345.1_ASM1419634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge250a15d-94c9-4c6c-8355-f429048083f1/dqc_reference/reference_markers.hmm GCF_014196345.1_ASM1419634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:11,481] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:11,482] [INFO] Found 6/6 markers.
[2024-01-24 13:13:11,529] [INFO] Query marker FASTA was written to GCF_014196345.1_ASM1419634v1_genomic.fna/markers.fasta
[2024-01-24 13:13:11,529] [INFO] Task started: Blastn
[2024-01-24 13:13:11,529] [INFO] Running command: blastn -query GCF_014196345.1_ASM1419634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge250a15d-94c9-4c6c-8355-f429048083f1/dqc_reference/reference_markers.fasta -out GCF_014196345.1_ASM1419634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:12,490] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:12,494] [INFO] Selected 12 target genomes.
[2024-01-24 13:13:12,494] [INFO] Target genome list was writen to GCF_014196345.1_ASM1419634v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:12,499] [INFO] Task started: fastANI
[2024-01-24 13:13:12,500] [INFO] Running command: fastANI --query /var/lib/cwl/stge353ddc0-3484-4415-8e15-2c58ffd022fe/GCF_014196345.1_ASM1419634v1_genomic.fna.gz --refList GCF_014196345.1_ASM1419634v1_genomic.fna/target_genomes.txt --output GCF_014196345.1_ASM1419634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:26,384] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:26,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge250a15d-94c9-4c6c-8355-f429048083f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:26,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge250a15d-94c9-4c6c-8355-f429048083f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:26,395] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:26,396] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:26,396] [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 brachythecii	strain=DSM 24105	GCA_014196345.1	1176177	1176177	type	True	100.0	1786	1787	95	conclusive
Methylobacterium gnaphalii	strain=NBRC 107716	GCA_007992215.1	1010610	1010610	type	True	86.8695	1153	1787	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	86.7711	1132	1787	95	below_threshold
Methylobacterium haplocladii	strain=NBRC 107714	GCA_007992175.1	1176176	1176176	type	True	84.4752	1078	1787	95	below_threshold
Methylobacterium haplocladii	strain=DSM 24195	GCA_022179265.1	1176176	1176176	type	True	84.4444	1046	1787	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	81.7852	749	1787	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	81.4899	913	1787	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	81.3083	774	1787	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	80.8735	903	1787	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	79.7435	805	1787	95	below_threshold
Methylobacterium frigidaeris	strain=IER25-16	GCA_002759055.1	2038277	2038277	type	True	79.5897	553	1787	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.2869	268	1787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:26,397] [INFO] DFAST Taxonomy check result was written to GCF_014196345.1_ASM1419634v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:26,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:26,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:26,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge250a15d-94c9-4c6c-8355-f429048083f1/dqc_reference/checkm_data
[2024-01-24 13:13:26,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:26,450] [INFO] Task started: CheckM
[2024-01-24 13:13:26,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196345.1_ASM1419634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196345.1_ASM1419634v1_genomic.fna/checkm_input GCF_014196345.1_ASM1419634v1_genomic.fna/checkm_result
[2024-01-24 13:14:13,987] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:13,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:14,009] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:14,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:14,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196345.1_ASM1419634v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:14,011] [INFO] Task started: Blastn
[2024-01-24 13:14:14,011] [INFO] Running command: blastn -query GCF_014196345.1_ASM1419634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge250a15d-94c9-4c6c-8355-f429048083f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196345.1_ASM1419634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:15,758] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:15,762] [INFO] Selected 11 target genomes.
[2024-01-24 13:14:15,762] [INFO] Target genome list was writen to GCF_014196345.1_ASM1419634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:15,772] [INFO] Task started: fastANI
[2024-01-24 13:14:15,772] [INFO] Running command: fastANI --query /var/lib/cwl/stge353ddc0-3484-4415-8e15-2c58ffd022fe/GCF_014196345.1_ASM1419634v1_genomic.fna.gz --refList GCF_014196345.1_ASM1419634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196345.1_ASM1419634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:29,076] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:29,092] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:29,092] [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_014196345.1	s__Methylobacterium brachythecii	100.0	1786	1787	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_007992215.1	s__Methylobacterium gnaphalii	86.8755	1152	1787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040035.1	s__Methylobacterium sp008040035	84.5426	1059	1787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992175.1	s__Methylobacterium haplocladii	84.5128	1072	1787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199935.1	s__Methylobacterium rhodinum	81.4211	955	1787	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	81.3618	869	1787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCA_002778835.1	s__Methylobacterium sp002778835	81.1732	805	1787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.93	99.92	0.96	0.96	4	-
GCF_008806345.1	s__Methylobacterium sp008806345	81.0958	891	1787	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	80.4006	848	1787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422815.1	s__Methylobacterium sp001422815	80.3828	782	1787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.57	97.58	0.90	0.88	3	-
GCF_008630155.1	s__Rhodovastum atsumiense	76.2113	263	1787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:29,094] [INFO] GTDB search result was written to GCF_014196345.1_ASM1419634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:29,095] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:29,098] [INFO] DFAST_QC result json was written to GCF_014196345.1_ASM1419634v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:29,098] [INFO] DFAST_QC completed!
[2024-01-24 13:14:29,099] [INFO] Total running time: 0h1m36s