[2024-01-24 10:48:09,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,177] [INFO] DQC Reference Directory: /var/lib/cwl/stgab660623-060f-46b0-88a8-b46a850c55b9/dqc_reference
[2024-01-24 10:48:23,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,955] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,955] [INFO] Running command: gunzip -c /var/lib/cwl/stga8f4e645-2e87-468e-8245-e5b661e7fc94/GCF_030160235.1_ASM3016023v1_genomic.fna.gz | prodigal -d GCF_030160235.1_ASM3016023v1_genomic.fna/cds.fna -a GCF_030160235.1_ASM3016023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:44,736] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:44,737] [INFO] Task started: HMMsearch
[2024-01-24 10:48:44,737] [INFO] Running command: hmmsearch --tblout GCF_030160235.1_ASM3016023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab660623-060f-46b0-88a8-b46a850c55b9/dqc_reference/reference_markers.hmm GCF_030160235.1_ASM3016023v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:45,070] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:45,072] [INFO] Found 6/6 markers.
[2024-01-24 10:48:45,128] [INFO] Query marker FASTA was written to GCF_030160235.1_ASM3016023v1_genomic.fna/markers.fasta
[2024-01-24 10:48:45,129] [INFO] Task started: Blastn
[2024-01-24 10:48:45,129] [INFO] Running command: blastn -query GCF_030160235.1_ASM3016023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab660623-060f-46b0-88a8-b46a850c55b9/dqc_reference/reference_markers.fasta -out GCF_030160235.1_ASM3016023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:46,204] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:46,208] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:46,209] [INFO] Target genome list was writen to GCF_030160235.1_ASM3016023v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:46,231] [INFO] Task started: fastANI
[2024-01-24 10:48:46,232] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f4e645-2e87-468e-8245-e5b661e7fc94/GCF_030160235.1_ASM3016023v1_genomic.fna.gz --refList GCF_030160235.1_ASM3016023v1_genomic.fna/target_genomes.txt --output GCF_030160235.1_ASM3016023v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:06,367] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:06,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab660623-060f-46b0-88a8-b46a850c55b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:06,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab660623-060f-46b0-88a8-b46a850c55b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:06,378] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:49:06,378] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:49:06,378] [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
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	94.0095	1830	2240	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	93.9956	1860	2240	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	93.6106	1819	2240	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	92.8838	1603	2240	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	91.5859	1798	2240	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	90.1123	1698	2240	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	87.7079	1639	2240	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.9237	1318	2240	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.1528	720	2240	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.1507	722	2240	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.9389	661	2240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:06,380] [INFO] DFAST Taxonomy check result was written to GCF_030160235.1_ASM3016023v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:06,382] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:06,382] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:06,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab660623-060f-46b0-88a8-b46a850c55b9/dqc_reference/checkm_data
[2024-01-24 10:49:06,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:06,465] [INFO] Task started: CheckM
[2024-01-24 10:49:06,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160235.1_ASM3016023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160235.1_ASM3016023v1_genomic.fna/checkm_input GCF_030160235.1_ASM3016023v1_genomic.fna/checkm_result
[2024-01-24 10:50:07,783] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:07,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:07,810] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:07,811] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:07,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160235.1_ASM3016023v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:07,812] [INFO] Task started: Blastn
[2024-01-24 10:50:07,812] [INFO] Running command: blastn -query GCF_030160235.1_ASM3016023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab660623-060f-46b0-88a8-b46a850c55b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160235.1_ASM3016023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:09,957] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:09,961] [INFO] Selected 8 target genomes.
[2024-01-24 10:50:09,961] [INFO] Target genome list was writen to GCF_030160235.1_ASM3016023v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:09,995] [INFO] Task started: fastANI
[2024-01-24 10:50:09,995] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f4e645-2e87-468e-8245-e5b661e7fc94/GCF_030160235.1_ASM3016023v1_genomic.fna.gz --refList GCF_030160235.1_ASM3016023v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160235.1_ASM3016023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:26,712] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:26,724] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:50:26,724] [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_003601985.1	s__Mesorhizobium jarvisii	94.0286	1828	2240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.40	98.93	0.96	0.91	10	-
GCF_000009625.1	s__Mesorhizobium japonicum	93.6333	1816	2240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.35	97.93	0.93	0.85	23	-
GCF_016467435.1	s__Mesorhizobium sp016467435	93.5487	1763	2240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.58	98.58	0.95	0.95	2	-
GCF_002295115.1	s__Mesorhizobium sp002295115	93.5259	1793	2240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.79	96.42	0.94	0.85	9	-
GCF_016756495.1	s__Mesorhizobium sp016756495	92.9068	1857	2240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879535.1	s__Mesorhizobium intechi	92.8763	1605	2240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014189455.1	s__Mesorhizobium huakuii_A	91.6915	1799	2240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353565.1	s__Mesorhizobium sp003353565	91.3747	1781	2240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:26,726] [INFO] GTDB search result was written to GCF_030160235.1_ASM3016023v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:26,727] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:26,730] [INFO] DFAST_QC result json was written to GCF_030160235.1_ASM3016023v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:26,730] [INFO] DFAST_QC completed!
[2024-01-24 10:50:26,730] [INFO] Total running time: 0h2m18s