[2024-01-24 14:28:16,104] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:16,113] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:16,114] [INFO] DQC Reference Directory: /var/lib/cwl/stgddeb5744-68df-474c-b4ee-fa8c8f992c3e/dqc_reference
[2024-01-24 14:28:17,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,939] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,939] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc7664e4-2768-45e1-95d4-39e6be4a0689/GCF_001653715.1_ASM165371v1_genomic.fna.gz | prodigal -d GCF_001653715.1_ASM165371v1_genomic.fna/cds.fna -a GCF_001653715.1_ASM165371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:35,597] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:35,597] [INFO] Task started: HMMsearch
[2024-01-24 14:28:35,597] [INFO] Running command: hmmsearch --tblout GCF_001653715.1_ASM165371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddeb5744-68df-474c-b4ee-fa8c8f992c3e/dqc_reference/reference_markers.hmm GCF_001653715.1_ASM165371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:35,909] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:35,910] [INFO] Found 6/6 markers.
[2024-01-24 14:28:35,964] [INFO] Query marker FASTA was written to GCF_001653715.1_ASM165371v1_genomic.fna/markers.fasta
[2024-01-24 14:28:35,965] [INFO] Task started: Blastn
[2024-01-24 14:28:35,965] [INFO] Running command: blastn -query GCF_001653715.1_ASM165371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddeb5744-68df-474c-b4ee-fa8c8f992c3e/dqc_reference/reference_markers.fasta -out GCF_001653715.1_ASM165371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:37,060] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:37,065] [INFO] Selected 18 target genomes.
[2024-01-24 14:28:37,065] [INFO] Target genome list was writen to GCF_001653715.1_ASM165371v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:37,078] [INFO] Task started: fastANI
[2024-01-24 14:28:37,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7664e4-2768-45e1-95d4-39e6be4a0689/GCF_001653715.1_ASM165371v1_genomic.fna.gz --refList GCF_001653715.1_ASM165371v1_genomic.fna/target_genomes.txt --output GCF_001653715.1_ASM165371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:09,158] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:09,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddeb5744-68df-474c-b4ee-fa8c8f992c3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:09,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddeb5744-68df-474c-b4ee-fa8c8f992c3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:09,173] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:29:09,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:29:09,173] [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 platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	100.0	2264	2268	95	conclusive
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	99.8228	1940	2268	95	conclusive
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	91.9963	1681	2268	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	91.1638	1792	2268	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	90.5715	1514	2268	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	90.4605	1719	2268	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	90.4308	1695	2268	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	90.3757	1599	2268	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	90.3412	1536	2268	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	90.0335	1698	2268	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	89.6838	1497	2268	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	85.0905	1465	2268	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	85.0137	1356	2268	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.7066	233	2268	95	below_threshold
Martelella radicis	strain=DSM 28101	GCA_014196625.1	1397476	1397476	type	True	76.6607	224	2268	95	below_threshold
Martelella endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	76.605	270	2268	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	76.0402	150	2268	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	76.0196	209	2268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:09,175] [INFO] DFAST Taxonomy check result was written to GCF_001653715.1_ASM165371v1_genomic.fna/tc_result.tsv
[2024-01-24 14:29:09,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:09,176] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:09,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddeb5744-68df-474c-b4ee-fa8c8f992c3e/dqc_reference/checkm_data
[2024-01-24 14:29:09,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:09,240] [INFO] Task started: CheckM
[2024-01-24 14:29:09,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001653715.1_ASM165371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001653715.1_ASM165371v1_genomic.fna/checkm_input GCF_001653715.1_ASM165371v1_genomic.fna/checkm_result
[2024-01-24 14:30:03,050] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:03,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:03,072] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:03,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:03,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001653715.1_ASM165371v1_genomic.fna/markers.fasta)
[2024-01-24 14:30:03,073] [INFO] Task started: Blastn
[2024-01-24 14:30:03,074] [INFO] Running command: blastn -query GCF_001653715.1_ASM165371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddeb5744-68df-474c-b4ee-fa8c8f992c3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001653715.1_ASM165371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:05,188] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:05,191] [INFO] Selected 18 target genomes.
[2024-01-24 14:30:05,192] [INFO] Target genome list was writen to GCF_001653715.1_ASM165371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:05,216] [INFO] Task started: fastANI
[2024-01-24 14:30:05,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7664e4-2768-45e1-95d4-39e6be4a0689/GCF_001653715.1_ASM165371v1_genomic.fna.gz --refList GCF_001653715.1_ASM165371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001653715.1_ASM165371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:41,130] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:41,146] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:41,147] [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_001653715.1	s__Methylobacterium platani	100.0	2264	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	conclusive
GCF_003173755.1	s__Methylobacterium terrae	91.9883	1682	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043735.1	s__Methylobacterium sp011043735	91.3299	1799	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151805.1	s__Methylobacterium sp006151805	91.1696	1792	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173775.1	s__Methylobacterium sp003173775	90.697	1689	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCA_019216885.1	s__Methylobacterium sp019216885	90.6606	1778	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016804325.1	s__Methylobacterium aquaticum_C	90.6566	1727	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043955.1	s__Methylobacterium tarhaniae	90.5681	1515	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058325.1	s__Methylobacterium currus	90.4388	1721	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613415.1	s__Methylobacterium ajmalii	90.4157	1594	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.55	96.20	0.90	0.83	5	-
GCF_001043895.1	s__Methylobacterium indicum	90.3452	1536	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.73	98.07	0.88	0.87	6	-
GCF_002759055.1	s__Methylobacterium frigidaeris	90.1963	1110	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745635.1	s__Methylobacterium sp004745635	90.0556	1697	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043975.1	s__Methylobacterium variabile	89.7019	1496	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105195.1	s__FEB-22 sp003105195	77.4297	521	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__FEB-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	77.3732	561	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861165.1	s__BOKV01 sp016861165	76.9421	395	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__BOKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000960975.1	s__Martelella endophytica	76.6295	267	2268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:41,149] [INFO] GTDB search result was written to GCF_001653715.1_ASM165371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:41,149] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:41,154] [INFO] DFAST_QC result json was written to GCF_001653715.1_ASM165371v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:41,154] [INFO] DFAST_QC completed!
[2024-01-24 14:30:41,154] [INFO] Total running time: 0h2m25s