[2024-01-24 13:41:40,292] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,294] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d90de67-9521-4dc5-8a39-927f9bb8cad4/dqc_reference
[2024-01-24 13:41:41,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:41,562] [INFO] Task started: Prodigal
[2024-01-24 13:41:41,563] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcd54aee-71fc-4720-a884-2fc61e9da997/GCF_900199455.1_ICMP_18942_genomic.fna.gz | prodigal -d GCF_900199455.1_ICMP_18942_genomic.fna/cds.fna -a GCF_900199455.1_ICMP_18942_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:42:07,640] [INFO] Task succeeded: Prodigal
[2024-01-24 13:42:07,641] [INFO] Task started: HMMsearch
[2024-01-24 13:42:07,641] [INFO] Running command: hmmsearch --tblout GCF_900199455.1_ICMP_18942_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d90de67-9521-4dc5-8a39-927f9bb8cad4/dqc_reference/reference_markers.hmm GCF_900199455.1_ICMP_18942_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:42:07,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:42:07,991] [INFO] Found 6/6 markers.
[2024-01-24 13:42:08,057] [INFO] Query marker FASTA was written to GCF_900199455.1_ICMP_18942_genomic.fna/markers.fasta
[2024-01-24 13:42:08,057] [INFO] Task started: Blastn
[2024-01-24 13:42:08,057] [INFO] Running command: blastn -query GCF_900199455.1_ICMP_18942_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d90de67-9521-4dc5-8a39-927f9bb8cad4/dqc_reference/reference_markers.fasta -out GCF_900199455.1_ICMP_18942_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:09,019] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:09,022] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:09,023] [INFO] Target genome list was writen to GCF_900199455.1_ICMP_18942_genomic.fna/target_genomes.txt
[2024-01-24 13:42:09,027] [INFO] Task started: fastANI
[2024-01-24 13:42:09,027] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcd54aee-71fc-4720-a884-2fc61e9da997/GCF_900199455.1_ICMP_18942_genomic.fna.gz --refList GCF_900199455.1_ICMP_18942_genomic.fna/target_genomes.txt --output GCF_900199455.1_ICMP_18942_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:30,106] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:30,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d90de67-9521-4dc5-8a39-927f9bb8cad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:30,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d90de67-9521-4dc5-8a39-927f9bb8cad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:30,130] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:30,131] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:30,131] [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 carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	100.0	2775	2783	95	conclusive
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	91.5396	1821	2783	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	91.3579	1859	2783	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	91.2391	1900	2783	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	90.5488	1583	2783	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	90.1357	1817	2783	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	87.9809	1858	2783	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	87.459	1736	2783	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.7746	1431	2783	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.026	654	2783	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.0199	750	2783	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.0184	750	2783	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:30,133] [INFO] DFAST Taxonomy check result was written to GCF_900199455.1_ICMP_18942_genomic.fna/tc_result.tsv
[2024-01-24 13:42:30,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:30,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:30,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d90de67-9521-4dc5-8a39-927f9bb8cad4/dqc_reference/checkm_data
[2024-01-24 13:42:30,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:30,217] [INFO] Task started: CheckM
[2024-01-24 13:42:30,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900199455.1_ICMP_18942_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900199455.1_ICMP_18942_genomic.fna/checkm_input GCF_900199455.1_ICMP_18942_genomic.fna/checkm_result
[2024-01-24 13:43:44,373] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:44,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:44,400] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:44,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:44,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900199455.1_ICMP_18942_genomic.fna/markers.fasta)
[2024-01-24 13:43:44,401] [INFO] Task started: Blastn
[2024-01-24 13:43:44,401] [INFO] Running command: blastn -query GCF_900199455.1_ICMP_18942_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d90de67-9521-4dc5-8a39-927f9bb8cad4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900199455.1_ICMP_18942_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:46,129] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:46,133] [INFO] Selected 10 target genomes.
[2024-01-24 13:43:46,133] [INFO] Target genome list was writen to GCF_900199455.1_ICMP_18942_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:46,365] [INFO] Task started: fastANI
[2024-01-24 13:43:46,365] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcd54aee-71fc-4720-a884-2fc61e9da997/GCF_900199455.1_ICMP_18942_genomic.fna.gz --refList GCF_900199455.1_ICMP_18942_genomic.fna/target_genomes_gtdb.txt --output GCF_900199455.1_ICMP_18942_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:06,276] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:06,295] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:06,295] [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_900199455.1	s__Mesorhizobium carmichaelinearum	100.0	2774	2783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014189455.1	s__Mesorhizobium huakuii_A	94.4631	2165	2783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356515.1	s__Mesorhizobium loti_C	93.2475	2160	2783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.70	98.70	0.94	0.94	2	-
GCF_003601985.1	s__Mesorhizobium jarvisii	91.547	1820	2783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.40	98.93	0.96	0.91	10	-
GCF_016467435.1	s__Mesorhizobium sp016467435	91.3006	1759	2783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.58	98.58	0.95	0.95	2	-
GCF_000009625.1	s__Mesorhizobium japonicum	91.2205	1902	2783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.35	97.93	0.93	0.85	23	-
GCF_016756495.1	s__Mesorhizobium sp016756495	91.1754	1959	2783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002295115.1	s__Mesorhizobium sp002295115	91.0725	1839	2783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.79	96.42	0.94	0.85	9	-
GCF_013170805.1	s__Mesorhizobium sp013170805	90.9595	1880	2783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002879535.1	s__Mesorhizobium intechi	90.5428	1584	2783	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 13:44:06,297] [INFO] GTDB search result was written to GCF_900199455.1_ICMP_18942_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:06,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:06,302] [INFO] DFAST_QC result json was written to GCF_900199455.1_ICMP_18942_genomic.fna/dqc_result.json
[2024-01-24 13:44:06,302] [INFO] DFAST_QC completed!
[2024-01-24 13:44:06,302] [INFO] Total running time: 0h2m26s