[2024-01-25 19:06:50,499] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:50,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:50,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgb42c024f-605b-4db5-bd28-fee22ce2a1da/dqc_reference
[2024-01-25 19:06:51,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:51,626] [INFO] Task started: Prodigal
[2024-01-25 19:06:51,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c177f1d-068c-434a-974e-b012718bdcf9/GCF_003148495.1_ASM314849v1_genomic.fna.gz | prodigal -d GCF_003148495.1_ASM314849v1_genomic.fna/cds.fna -a GCF_003148495.1_ASM314849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:12,180] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:12,181] [INFO] Task started: HMMsearch
[2024-01-25 19:07:12,181] [INFO] Running command: hmmsearch --tblout GCF_003148495.1_ASM314849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb42c024f-605b-4db5-bd28-fee22ce2a1da/dqc_reference/reference_markers.hmm GCF_003148495.1_ASM314849v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:12,524] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:12,526] [INFO] Found 6/6 markers.
[2024-01-25 19:07:12,588] [INFO] Query marker FASTA was written to GCF_003148495.1_ASM314849v1_genomic.fna/markers.fasta
[2024-01-25 19:07:12,588] [INFO] Task started: Blastn
[2024-01-25 19:07:12,588] [INFO] Running command: blastn -query GCF_003148495.1_ASM314849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb42c024f-605b-4db5-bd28-fee22ce2a1da/dqc_reference/reference_markers.fasta -out GCF_003148495.1_ASM314849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:13,626] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:13,629] [INFO] Selected 15 target genomes.
[2024-01-25 19:07:13,629] [INFO] Target genome list was writen to GCF_003148495.1_ASM314849v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:13,645] [INFO] Task started: fastANI
[2024-01-25 19:07:13,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c177f1d-068c-434a-974e-b012718bdcf9/GCF_003148495.1_ASM314849v1_genomic.fna.gz --refList GCF_003148495.1_ASM314849v1_genomic.fna/target_genomes.txt --output GCF_003148495.1_ASM314849v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:38,934] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:38,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb42c024f-605b-4db5-bd28-fee22ce2a1da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:38,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb42c024f-605b-4db5-bd28-fee22ce2a1da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:38,945] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:07:38,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:38,945] [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 loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	100.0	2456	2456	95	conclusive
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	93.818	1878	2456	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	89.5028	1685	2456	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	89.3803	1683	2456	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	89.2669	1681	2456	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	87.9885	1725	2456	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	87.9436	1711	2456	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	87.8633	1663	2456	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	87.823	1761	2456	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	86.3741	1351	2456	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	86.3332	1598	2456	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	85.2772	1393	2456	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.0669	654	2456	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.9335	699	2456	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9197	702	2456	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:38,947] [INFO] DFAST Taxonomy check result was written to GCF_003148495.1_ASM314849v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:38,947] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:38,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:38,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb42c024f-605b-4db5-bd28-fee22ce2a1da/dqc_reference/checkm_data
[2024-01-25 19:07:38,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:39,015] [INFO] Task started: CheckM
[2024-01-25 19:07:39,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148495.1_ASM314849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148495.1_ASM314849v1_genomic.fna/checkm_input GCF_003148495.1_ASM314849v1_genomic.fna/checkm_result
[2024-01-25 19:08:37,594] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:37,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:37,621] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:37,621] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:37,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148495.1_ASM314849v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:37,622] [INFO] Task started: Blastn
[2024-01-25 19:08:37,622] [INFO] Running command: blastn -query GCF_003148495.1_ASM314849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb42c024f-605b-4db5-bd28-fee22ce2a1da/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148495.1_ASM314849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:39,692] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:39,695] [INFO] Selected 11 target genomes.
[2024-01-25 19:08:39,696] [INFO] Target genome list was writen to GCF_003148495.1_ASM314849v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:39,709] [INFO] Task started: fastANI
[2024-01-25 19:08:39,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c177f1d-068c-434a-974e-b012718bdcf9/GCF_003148495.1_ASM314849v1_genomic.fna.gz --refList GCF_003148495.1_ASM314849v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148495.1_ASM314849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:59,692] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:59,700] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:59,701] [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_003148495.1	s__Mesorhizobium loti	100.0	2456	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.10	97.93	0.88	0.86	3	conclusive
GCF_004919685.1	s__Mesorhizobium norvegicum	93.8077	1879	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.97	99.97	0.98	0.98	2	-
GCA_014189435.1	s__Mesorhizobium loti_G	93.3984	1894	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425625.1	s__Mesorhizobium sp001425625	93.1959	1676	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.21	99.21	0.90	0.90	2	-
GCF_000519305.1	s__Mesorhizobium ciceri_B	91.5262	1706	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003997495.1	s__Mesorhizobium sp003997495	91.4955	1685	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003997935.1	s__Mesorhizobium sp003997935	91.2502	1562	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004017275.1	s__Mesorhizobium sp004017275	91.2211	1580	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.13	97.50	0.90	0.85	4	-
GCF_000185905.1	s__Mesorhizobium ciceri	91.1774	1734	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.42	98.05	0.90	0.85	36	-
GCF_003996995.1	s__Mesorhizobium sp003996995	90.9194	1352	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.83	97.35	0.87	0.74	32	-
GCF_000502955.1	s__Mesorhizobium sp000502955	90.0236	1616	2456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:08:59,702] [INFO] GTDB search result was written to GCF_003148495.1_ASM314849v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:59,702] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:59,706] [INFO] DFAST_QC result json was written to GCF_003148495.1_ASM314849v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:59,706] [INFO] DFAST_QC completed!
[2024-01-25 19:08:59,706] [INFO] Total running time: 0h2m9s