[2024-01-24 13:12:56,131] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,134] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,134] [INFO] DQC Reference Directory: /var/lib/cwl/stgeef54184-33a5-422d-beec-fa831fc74cf7/dqc_reference
[2024-01-24 13:12:57,550] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,551] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,552] [INFO] Running command: gunzip -c /var/lib/cwl/stge9ab4697-f549-48d5-b2ec-448659d02475/GCF_002937075.1_ASM293707v1_genomic.fna.gz | prodigal -d GCF_002937075.1_ASM293707v1_genomic.fna/cds.fna -a GCF_002937075.1_ASM293707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:12,896] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:12,896] [INFO] Task started: HMMsearch
[2024-01-24 13:13:12,896] [INFO] Running command: hmmsearch --tblout GCF_002937075.1_ASM293707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeef54184-33a5-422d-beec-fa831fc74cf7/dqc_reference/reference_markers.hmm GCF_002937075.1_ASM293707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:13,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:13,218] [INFO] Found 6/6 markers.
[2024-01-24 13:13:13,264] [INFO] Query marker FASTA was written to GCF_002937075.1_ASM293707v1_genomic.fna/markers.fasta
[2024-01-24 13:13:13,264] [INFO] Task started: Blastn
[2024-01-24 13:13:13,264] [INFO] Running command: blastn -query GCF_002937075.1_ASM293707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeef54184-33a5-422d-beec-fa831fc74cf7/dqc_reference/reference_markers.fasta -out GCF_002937075.1_ASM293707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:14,233] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:14,237] [INFO] Selected 10 target genomes.
[2024-01-24 13:13:14,237] [INFO] Target genome list was writen to GCF_002937075.1_ASM293707v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:14,243] [INFO] Task started: fastANI
[2024-01-24 13:13:14,244] [INFO] Running command: fastANI --query /var/lib/cwl/stge9ab4697-f549-48d5-b2ec-448659d02475/GCF_002937075.1_ASM293707v1_genomic.fna.gz --refList GCF_002937075.1_ASM293707v1_genomic.fna/target_genomes.txt --output GCF_002937075.1_ASM293707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:26,659] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:26,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeef54184-33a5-422d-beec-fa831fc74cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:26,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeef54184-33a5-422d-beec-fa831fc74cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:26,669] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:26,669] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:26,669] [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
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_002937075.1	333368	333368	type	True	100.0	1625	1630	95	conclusive
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_014197735.1	333368	333368	type	True	99.9692	1596	1630	95	conclusive
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	84.9801	1023	1630	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	84.9489	987	1630	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_900187365.1	1074	1074	suspected-type	True	84.9148	1025	1630	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	79.6766	608	1630	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.1414	307	1630	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.8866	279	1630	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.773	244	1630	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	76.6874	296	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:26,671] [INFO] DFAST Taxonomy check result was written to GCF_002937075.1_ASM293707v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:26,671] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:26,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:26,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeef54184-33a5-422d-beec-fa831fc74cf7/dqc_reference/checkm_data
[2024-01-24 13:13:26,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:26,727] [INFO] Task started: CheckM
[2024-01-24 13:13:26,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002937075.1_ASM293707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002937075.1_ASM293707v1_genomic.fna/checkm_input GCF_002937075.1_ASM293707v1_genomic.fna/checkm_result
[2024-01-24 13:14:12,580] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:12,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:12,603] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:12,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:12,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002937075.1_ASM293707v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:12,605] [INFO] Task started: Blastn
[2024-01-24 13:14:12,605] [INFO] Running command: blastn -query GCF_002937075.1_ASM293707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeef54184-33a5-422d-beec-fa831fc74cf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002937075.1_ASM293707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:14,466] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:14,470] [INFO] Selected 7 target genomes.
[2024-01-24 13:14:14,471] [INFO] Target genome list was writen to GCF_002937075.1_ASM293707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:14,479] [INFO] Task started: fastANI
[2024-01-24 13:14:14,479] [INFO] Running command: fastANI --query /var/lib/cwl/stge9ab4697-f549-48d5-b2ec-448659d02475/GCF_002937075.1_ASM293707v1_genomic.fna.gz --refList GCF_002937075.1_ASM293707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002937075.1_ASM293707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:22,505] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:22,516] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:22,517] [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_002937075.1	s__Rhodoblastus sphagnicola	100.0	1625	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_900187365.1	s__Rhodoblastus acidophilus	84.8989	1027	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	99.99	99.99	0.99	0.99	3	-
GCF_009720655.1	s__Rhodoblastus acidophilus_A	83.7954	894	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197695.1	s__Rhodoblastus acidophilus_B	83.4718	938	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903185.1	s__Rhodoblastus sp903903185	79.8419	631	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745395.1	s__Methylocystis sp016745395	77.6487	286	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427445.1	s__Methylocella acidiphila	77.1247	217	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:22,518] [INFO] GTDB search result was written to GCF_002937075.1_ASM293707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:22,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:22,523] [INFO] DFAST_QC result json was written to GCF_002937075.1_ASM293707v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:22,523] [INFO] DFAST_QC completed!
[2024-01-24 13:14:22,523] [INFO] Total running time: 0h1m26s