[2023-06-28 10:47:03,033] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:47:03,036] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:47:03,037] [INFO] DQC Reference Directory: /var/lib/cwl/stgfee59473-e88b-48e2-b384-03c9e04295a9/dqc_reference
[2023-06-28 10:47:05,217] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:47:05,218] [INFO] Task started: Prodigal
[2023-06-28 10:47:05,218] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a77e0bf-5acb-4041-9aeb-de3e09f0d7a7/GCA_005144675.1_ASM514467v1_genomic.fna.gz | prodigal -d GCA_005144675.1_ASM514467v1_genomic.fna/cds.fna -a GCA_005144675.1_ASM514467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:47:23,084] [INFO] Task succeeded: Prodigal
[2023-06-28 10:47:23,085] [INFO] Task started: HMMsearch
[2023-06-28 10:47:23,085] [INFO] Running command: hmmsearch --tblout GCA_005144675.1_ASM514467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfee59473-e88b-48e2-b384-03c9e04295a9/dqc_reference/reference_markers.hmm GCA_005144675.1_ASM514467v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:47:23,410] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:47:23,415] [INFO] Found 6/6 markers.
[2023-06-28 10:47:23,499] [INFO] Query marker FASTA was written to GCA_005144675.1_ASM514467v1_genomic.fna/markers.fasta
[2023-06-28 10:47:23,500] [INFO] Task started: Blastn
[2023-06-28 10:47:23,500] [INFO] Running command: blastn -query GCA_005144675.1_ASM514467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee59473-e88b-48e2-b384-03c9e04295a9/dqc_reference/reference_markers.fasta -out GCA_005144675.1_ASM514467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:24,621] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:24,625] [INFO] Selected 14 target genomes.
[2023-06-28 10:47:24,626] [INFO] Target genome list was writen to GCA_005144675.1_ASM514467v1_genomic.fna/target_genomes.txt
[2023-06-28 10:47:24,630] [INFO] Task started: fastANI
[2023-06-28 10:47:24,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a77e0bf-5acb-4041-9aeb-de3e09f0d7a7/GCA_005144675.1_ASM514467v1_genomic.fna.gz --refList GCA_005144675.1_ASM514467v1_genomic.fna/target_genomes.txt --output GCA_005144675.1_ASM514467v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:47:45,308] [INFO] Task succeeded: fastANI
[2023-06-28 10:47:45,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfee59473-e88b-48e2-b384-03c9e04295a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:47:45,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfee59473-e88b-48e2-b384-03c9e04295a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:47:45,324] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 10:47:45,324] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 10:47:45,324] [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 wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	95.7011	1580	1902	95	conclusive
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	93.1017	1551	1902	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	93.0335	1561	1902	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	92.4445	1531	1902	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	87.3162	1225	1902	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	86.8272	1253	1902	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	84.8143	1226	1902	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	84.6133	1196	1902	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	84.5767	1218	1902	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	84.5218	1123	1902	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	83.8409	1072	1902	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.9663	608	1902	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.9623	556	1902	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9411	611	1902	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:47:45,326] [INFO] DFAST Taxonomy check result was written to GCA_005144675.1_ASM514467v1_genomic.fna/tc_result.tsv
[2023-06-28 10:47:45,326] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:47:45,327] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:47:45,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfee59473-e88b-48e2-b384-03c9e04295a9/dqc_reference/checkm_data
[2023-06-28 10:47:45,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:47:45,390] [INFO] Task started: CheckM
[2023-06-28 10:47:45,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005144675.1_ASM514467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005144675.1_ASM514467v1_genomic.fna/checkm_input GCA_005144675.1_ASM514467v1_genomic.fna/checkm_result
[2023-06-28 10:48:36,825] [INFO] Task succeeded: CheckM
[2023-06-28 10:48:36,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 1.56%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-28 10:48:36,856] [INFO] ===== Completeness check finished =====
[2023-06-28 10:48:36,856] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:48:36,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005144675.1_ASM514467v1_genomic.fna/markers.fasta)
[2023-06-28 10:48:36,857] [INFO] Task started: Blastn
[2023-06-28 10:48:36,857] [INFO] Running command: blastn -query GCA_005144675.1_ASM514467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee59473-e88b-48e2-b384-03c9e04295a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_005144675.1_ASM514467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:48:38,929] [INFO] Task succeeded: Blastn
[2023-06-28 10:48:38,934] [INFO] Selected 10 target genomes.
[2023-06-28 10:48:38,935] [INFO] Target genome list was writen to GCA_005144675.1_ASM514467v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:48:38,943] [INFO] Task started: fastANI
[2023-06-28 10:48:38,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a77e0bf-5acb-4041-9aeb-de3e09f0d7a7/GCA_005144675.1_ASM514467v1_genomic.fna.gz --refList GCA_005144675.1_ASM514467v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005144675.1_ASM514467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:48:55,607] [INFO] Task succeeded: fastANI
[2023-06-28 10:48:55,621] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:48:55,622] [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_002284535.1	s__Mesorhizobium wenxiniae	95.7061	1580	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.50	95.53	0.83	0.79	62	conclusive
GCA_004020645.1	s__Mesorhizobium sp004020645	93.1321	1572	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCF_002284575.1	s__Mesorhizobium temperatum	93.0335	1561	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.74	95.09	0.81	0.81	3	-
GCA_004020315.1	s__Mesorhizobium sp004020315	93.0325	1531	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.08	99.08	0.89	0.89	2	-
GCF_900099905.1	s__Mesorhizobium muleiense	92.4481	1530	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	-
GCF_002284565.1	s__Mesorhizobium mediterraneum_A	92.3537	1513	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.16	97.72	0.92	0.89	20	-
GCA_004020365.1	s__Mesorhizobium sp004020365	92.2535	1536	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.10	96.06	0.82	0.80	8	-
GCF_900156895.1	s__Mesorhizobium prunaredense	92.0732	1441	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756595.1	s__Mesorhizobium sp004020105	91.643	1511	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	-
GCF_007830515.1	s__Mesorhizobium tianshanense	90.5483	1403	1902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:48:55,623] [INFO] GTDB search result was written to GCA_005144675.1_ASM514467v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:48:55,624] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:48:55,628] [INFO] DFAST_QC result json was written to GCA_005144675.1_ASM514467v1_genomic.fna/dqc_result.json
[2023-06-28 10:48:55,628] [INFO] DFAST_QC completed!
[2023-06-28 10:48:55,628] [INFO] Total running time: 0h1m53s