[2024-01-25 18:45:05,597] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:05,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:05,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf9684ac-060d-4130-8fcc-0db21052630d/dqc_reference
[2024-01-25 18:45:06,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:06,768] [INFO] Task started: Prodigal
[2024-01-25 18:45:06,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ddbaa87-4fb9-402d-9382-81db1255a87e/GCF_014845095.1_ASM1484509v1_genomic.fna.gz | prodigal -d GCF_014845095.1_ASM1484509v1_genomic.fna/cds.fna -a GCF_014845095.1_ASM1484509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:17,899] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:17,899] [INFO] Task started: HMMsearch
[2024-01-25 18:45:17,899] [INFO] Running command: hmmsearch --tblout GCF_014845095.1_ASM1484509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf9684ac-060d-4130-8fcc-0db21052630d/dqc_reference/reference_markers.hmm GCF_014845095.1_ASM1484509v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:18,137] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:18,138] [INFO] Found 6/6 markers.
[2024-01-25 18:45:18,178] [INFO] Query marker FASTA was written to GCF_014845095.1_ASM1484509v1_genomic.fna/markers.fasta
[2024-01-25 18:45:18,178] [INFO] Task started: Blastn
[2024-01-25 18:45:18,179] [INFO] Running command: blastn -query GCF_014845095.1_ASM1484509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf9684ac-060d-4130-8fcc-0db21052630d/dqc_reference/reference_markers.fasta -out GCF_014845095.1_ASM1484509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:19,081] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:19,084] [INFO] Selected 14 target genomes.
[2024-01-25 18:45:19,084] [INFO] Target genome list was writen to GCF_014845095.1_ASM1484509v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:19,097] [INFO] Task started: fastANI
[2024-01-25 18:45:19,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ddbaa87-4fb9-402d-9382-81db1255a87e/GCF_014845095.1_ASM1484509v1_genomic.fna.gz --refList GCF_014845095.1_ASM1484509v1_genomic.fna/target_genomes.txt --output GCF_014845095.1_ASM1484509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:34,580] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:34,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf9684ac-060d-4130-8fcc-0db21052630d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:34,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf9684ac-060d-4130-8fcc-0db21052630d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:34,590] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:45:34,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:34,590] [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 bullatum	strain=LMG 24788	GCA_014845095.1	570505	570505	type	True	100.0	1473	1483	95	conclusive
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	99.9844	1468	1483	95	conclusive
Methylobacterium marchantiae	strain=DSM 21328	GCA_022179405.1	600331	600331	type	True	87.6078	1120	1483	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	82.4198	860	1483	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	82.409	874	1483	95	below_threshold
Methylobacterium gossipiicola	strain=Gh-105	GCA_900113485.1	582675	582675	type	True	82.319	842	1483	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	81.8841	776	1483	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	81.3768	823	1483	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.3493	665	1483	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	81.016	670	1483	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	80.9422	819	1483	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	80.0698	726	1483	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	80.038	754	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:34,593] [INFO] DFAST Taxonomy check result was written to GCF_014845095.1_ASM1484509v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:34,593] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:34,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:34,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf9684ac-060d-4130-8fcc-0db21052630d/dqc_reference/checkm_data
[2024-01-25 18:45:34,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:34,645] [INFO] Task started: CheckM
[2024-01-25 18:45:34,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014845095.1_ASM1484509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014845095.1_ASM1484509v1_genomic.fna/checkm_input GCF_014845095.1_ASM1484509v1_genomic.fna/checkm_result
[2024-01-25 18:46:09,185] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:09,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:09,214] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:09,214] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:09,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014845095.1_ASM1484509v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:09,215] [INFO] Task started: Blastn
[2024-01-25 18:46:09,215] [INFO] Running command: blastn -query GCF_014845095.1_ASM1484509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf9684ac-060d-4130-8fcc-0db21052630d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014845095.1_ASM1484509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:10,867] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:10,870] [INFO] Selected 19 target genomes.
[2024-01-25 18:46:10,870] [INFO] Target genome list was writen to GCF_014845095.1_ASM1484509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:10,898] [INFO] Task started: fastANI
[2024-01-25 18:46:10,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ddbaa87-4fb9-402d-9382-81db1255a87e/GCF_014845095.1_ASM1484509v1_genomic.fna.gz --refList GCF_014845095.1_ASM1484509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014845095.1_ASM1484509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:32,590] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:32,601] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:32,601] [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_014845095.1	s__Methylobacterium bullatum	100.0	1473	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.58	95.73	0.88	0.87	6	conclusive
GCF_000519085.1	s__Methylobacterium sp000519085	92.6054	1284	1483	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	90.6906	1236	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.57	97.58	0.90	0.88	3	-
GCF_000372825.1	s__Methylobacterium sp000372825	87.8057	1134	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422375.1	s__Methylobacterium sp001422375	83.023	906	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.25	0.90	0.90	2	-
GCF_001423295.1	s__Methylobacterium sp001423295	82.7589	882	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.75	98.70	0.92	0.92	5	-
GCF_001422885.1	s__Methylobacterium sp001422885	82.7281	933	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424705.1	s__Methylobacterium sp001424705	82.6211	920	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.56	98.52	0.92	0.91	5	-
GCF_003217615.1	s__Methylobacterium sp003217615	82.5625	924	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001423265.1	s__Methylobacterium sp001423265	82.4244	859	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.73	0.95	0.94	3	-
GCF_900113485.1	s__Methylobacterium gossipiicola	82.3352	840	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806385.1	s__Methylobacterium soli	81.5197	830	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425465.1	s__Methylobacterium sp001425465	80.9757	824	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111705.1	s__Methylobacterium sp003111705	80.6436	818	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.28	97.28	0.88	0.88	3	-
GCF_014873335.1	s__Methylobacterium sp014873335	80.4846	726	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004004555.2	s__Methylobacterium sp004004555	80.0545	728	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873545.1	s__OAS926 sp014873545	76.8495	209	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__OAS926	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390865.1	s__HLUCCA09 sp003390865	76.1461	122	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:32,602] [INFO] GTDB search result was written to GCF_014845095.1_ASM1484509v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:32,603] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:32,606] [INFO] DFAST_QC result json was written to GCF_014845095.1_ASM1484509v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:32,606] [INFO] DFAST_QC completed!
[2024-01-25 18:46:32,606] [INFO] Total running time: 0h1m27s