[2024-01-24 14:07:31,060] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:31,062] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:31,062] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6fe7166-dc3a-49d7-a00b-d69908632a49/dqc_reference
[2024-01-24 14:07:32,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:32,345] [INFO] Task started: Prodigal
[2024-01-24 14:07:32,346] [INFO] Running command: gunzip -c /var/lib/cwl/stga97413a9-e269-42a0-aa13-b50d3c22a268/GCF_013520985.1_ASM1352098v1_genomic.fna.gz | prodigal -d GCF_013520985.1_ASM1352098v1_genomic.fna/cds.fna -a GCF_013520985.1_ASM1352098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:54,414] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:54,415] [INFO] Task started: HMMsearch
[2024-01-24 14:07:54,415] [INFO] Running command: hmmsearch --tblout GCF_013520985.1_ASM1352098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6fe7166-dc3a-49d7-a00b-d69908632a49/dqc_reference/reference_markers.hmm GCF_013520985.1_ASM1352098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:54,753] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:54,754] [INFO] Found 6/6 markers.
[2024-01-24 14:07:54,816] [INFO] Query marker FASTA was written to GCF_013520985.1_ASM1352098v1_genomic.fna/markers.fasta
[2024-01-24 14:07:54,816] [INFO] Task started: Blastn
[2024-01-24 14:07:54,816] [INFO] Running command: blastn -query GCF_013520985.1_ASM1352098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6fe7166-dc3a-49d7-a00b-d69908632a49/dqc_reference/reference_markers.fasta -out GCF_013520985.1_ASM1352098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:55,847] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:55,852] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:55,852] [INFO] Target genome list was writen to GCF_013520985.1_ASM1352098v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:55,861] [INFO] Task started: fastANI
[2024-01-24 14:07:55,861] [INFO] Running command: fastANI --query /var/lib/cwl/stga97413a9-e269-42a0-aa13-b50d3c22a268/GCF_013520985.1_ASM1352098v1_genomic.fna.gz --refList GCF_013520985.1_ASM1352098v1_genomic.fna/target_genomes.txt --output GCF_013520985.1_ASM1352098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:27,774] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:27,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6fe7166-dc3a-49d7-a00b-d69908632a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:27,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6fe7166-dc3a-49d7-a00b-d69908632a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:27,793] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:08:27,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:08:27,794] [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 neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	100.0	2403	2405	95	conclusive
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	91.5312	1742	2405	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	86.4499	1581	2405	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	86.2722	1610	2405	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	86.1505	1484	2405	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	86.1449	1653	2405	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	86.0482	1556	2405	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	85.9439	1492	2405	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	85.7036	1444	2405	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	85.6751	1377	2405	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	85.4465	1323	2405	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	85.1554	1449	2405	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	85.0987	1412	2405	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	84.9443	1506	2405	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	84.8043	1347	2405	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.7912	1407	2405	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.1421	658	2405	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.0732	703	2405	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.8274	664	2405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:27,796] [INFO] DFAST Taxonomy check result was written to GCF_013520985.1_ASM1352098v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:27,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:27,797] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:27,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6fe7166-dc3a-49d7-a00b-d69908632a49/dqc_reference/checkm_data
[2024-01-24 14:08:27,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:27,879] [INFO] Task started: CheckM
[2024-01-24 14:08:27,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013520985.1_ASM1352098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013520985.1_ASM1352098v1_genomic.fna/checkm_input GCF_013520985.1_ASM1352098v1_genomic.fna/checkm_result
[2024-01-24 14:09:30,820] [INFO] Task succeeded: CheckM
[2024-01-24 14:09:30,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:09:30,844] [INFO] ===== Completeness check finished =====
[2024-01-24 14:09:30,844] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:09:30,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013520985.1_ASM1352098v1_genomic.fna/markers.fasta)
[2024-01-24 14:09:30,845] [INFO] Task started: Blastn
[2024-01-24 14:09:30,845] [INFO] Running command: blastn -query GCF_013520985.1_ASM1352098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6fe7166-dc3a-49d7-a00b-d69908632a49/dqc_reference/reference_markers_gtdb.fasta -out GCF_013520985.1_ASM1352098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:09:32,927] [INFO] Task succeeded: Blastn
[2024-01-24 14:09:32,931] [INFO] Selected 9 target genomes.
[2024-01-24 14:09:32,931] [INFO] Target genome list was writen to GCF_013520985.1_ASM1352098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:09:32,943] [INFO] Task started: fastANI
[2024-01-24 14:09:32,944] [INFO] Running command: fastANI --query /var/lib/cwl/stga97413a9-e269-42a0-aa13-b50d3c22a268/GCF_013520985.1_ASM1352098v1_genomic.fna.gz --refList GCF_013520985.1_ASM1352098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013520985.1_ASM1352098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:50,319] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:50,331] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:50,331] [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_013520985.1	s__Mesorhizobium sp013520985	100.0	2403	2405	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_016836705.1	s__Mesorhizobium caraganae	91.5311	1742	2405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	96.20	0.88	0.86	3	-
GCF_007003975.1	s__Mesorhizobium sp007003975	91.3996	1733	2405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000502715.1	s__Mesorhizobium sp000502715	90.8064	1582	2405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.12	97.73	0.92	0.90	39	-
GCA_900472295.1	s__Mesorhizobium sp900472295	90.4059	1604	2405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.35	97.33	0.92	0.92	3	-
GCF_016756535.1	s__Mesorhizobium sp016756535	86.0069	1599	2405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176035.2	s__Mesorhizobium opportunistum	85.9165	1497	2405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.26	95.55	0.85	0.80	10	-
GCF_018588885.1	s__Mesorhizobium sp018588885	85.7141	1512	2405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952505.1	s__Mesorhizobium sp003952505	85.6322	1531	2405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:50,333] [INFO] GTDB search result was written to GCF_013520985.1_ASM1352098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:50,333] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:50,337] [INFO] DFAST_QC result json was written to GCF_013520985.1_ASM1352098v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:50,337] [INFO] DFAST_QC completed!
[2024-01-24 14:09:50,337] [INFO] Total running time: 0h2m19s