[2024-01-24 12:44:11,218] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,219] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg41c4a039-8c95-41a8-8fed-dba141ff25b2/dqc_reference
[2024-01-24 12:44:12,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,657] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,657] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8d43be2-27f0-4d59-bfb8-c3f2c9c246e8/GCF_006516965.1_ASM651696v1_genomic.fna.gz | prodigal -d GCF_006516965.1_ASM651696v1_genomic.fna/cds.fna -a GCF_006516965.1_ASM651696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:23,648] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:23,649] [INFO] Task started: HMMsearch
[2024-01-24 12:44:23,649] [INFO] Running command: hmmsearch --tblout GCF_006516965.1_ASM651696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41c4a039-8c95-41a8-8fed-dba141ff25b2/dqc_reference/reference_markers.hmm GCF_006516965.1_ASM651696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:24,013] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:24,014] [INFO] Found 6/6 markers.
[2024-01-24 12:44:24,049] [INFO] Query marker FASTA was written to GCF_006516965.1_ASM651696v1_genomic.fna/markers.fasta
[2024-01-24 12:44:24,049] [INFO] Task started: Blastn
[2024-01-24 12:44:24,050] [INFO] Running command: blastn -query GCF_006516965.1_ASM651696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41c4a039-8c95-41a8-8fed-dba141ff25b2/dqc_reference/reference_markers.fasta -out GCF_006516965.1_ASM651696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:25,076] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:25,080] [INFO] Selected 22 target genomes.
[2024-01-24 12:44:25,080] [INFO] Target genome list was writen to GCF_006516965.1_ASM651696v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:25,092] [INFO] Task started: fastANI
[2024-01-24 12:44:25,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d43be2-27f0-4d59-bfb8-c3f2c9c246e8/GCF_006516965.1_ASM651696v1_genomic.fna.gz --refList GCF_006516965.1_ASM651696v1_genomic.fna/target_genomes.txt --output GCF_006516965.1_ASM651696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:45,057] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:45,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41c4a039-8c95-41a8-8fed-dba141ff25b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:45,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41c4a039-8c95-41a8-8fed-dba141ff25b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:45,074] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:45,074] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:45,075] [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
Pararhizobium mangrovi	strain=BGMRC 6574	GCA_006516965.1	2590452	2590452	type	True	100.0	1272	1274	95	conclusive
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.9803	477	1274	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	78.8062	465	1274	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.4547	363	1274	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.3272	494	1274	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	78.2839	423	1274	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.2751	415	1274	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	78.1706	428	1274	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	78.0988	365	1274	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	77.9374	400	1274	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	77.8869	336	1274	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	77.8208	308	1274	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_008932245.1	1752398	1752398	type	True	77.7975	340	1274	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	77.7728	339	1274	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	77.7616	359	1274	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_001723275.1	1752398	1752398	type	True	77.7488	344	1274	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	77.7461	359	1274	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	77.6347	355	1274	95	below_threshold
Pararhizobium antarcticum	strain=NAQVI 59	GCA_001885585.1	1798805	1798805	type	True	77.3841	318	1274	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	76.8761	201	1274	95	below_threshold
Phyllobacterium myrsinacearum	strain=IAM 13584	GCA_003182235.1	28101	28101	type	True	76.861	203	1274	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_004217385.1	28101	28101	type	True	76.8211	205	1274	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:45,076] [INFO] DFAST Taxonomy check result was written to GCF_006516965.1_ASM651696v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:45,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:45,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:45,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41c4a039-8c95-41a8-8fed-dba141ff25b2/dqc_reference/checkm_data
[2024-01-24 12:44:45,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:45,125] [INFO] Task started: CheckM
[2024-01-24 12:44:45,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006516965.1_ASM651696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006516965.1_ASM651696v1_genomic.fna/checkm_input GCF_006516965.1_ASM651696v1_genomic.fna/checkm_result
[2024-01-24 12:45:20,293] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:20,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:20,321] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:20,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:20,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006516965.1_ASM651696v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:20,322] [INFO] Task started: Blastn
[2024-01-24 12:45:20,322] [INFO] Running command: blastn -query GCF_006516965.1_ASM651696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41c4a039-8c95-41a8-8fed-dba141ff25b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_006516965.1_ASM651696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:22,382] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:22,386] [INFO] Selected 24 target genomes.
[2024-01-24 12:45:22,386] [INFO] Target genome list was writen to GCF_006516965.1_ASM651696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:22,427] [INFO] Task started: fastANI
[2024-01-24 12:45:22,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d43be2-27f0-4d59-bfb8-c3f2c9c246e8/GCF_006516965.1_ASM651696v1_genomic.fna.gz --refList GCF_006516965.1_ASM651696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006516965.1_ASM651696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:46,720] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:46,744] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:46,745] [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_006516965.1	s__Pararhizobium_B mangrovi	100.0	1272	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014203155.1	s__Shinella fusca	78.8103	463	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839145.1	s__Shinella sp016839145	78.7208	445	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469965.1	s__Mycoplana sp900469965	78.5649	436	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	98.03	97.96	0.94	0.92	10	-
GCF_004341885.1	s__Shinella granuli	78.5078	461	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_000497755.1	s__Aliihoeflea sp000497755	78.378	346	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742175.1	s__Aliihoeflea sp016742175	78.2098	392	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	78.1828	425	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	78.0745	396	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177415.1	s__Neorhizobium oryzae_A	78.0448	393	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004354915.1	s__Pseudohoeflea suaedae	77.9997	315	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940685.1	s__Ensifer adhaerens_E	77.9856	394	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283665.1	s__Ensifer sesbaniae	77.9291	399	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.93	98.93	0.89	0.89	2	-
GCF_000759435.1	s__Hoeflea sp000759435	77.9157	391	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513895.1	s__Sinorhizobium sp000513895	77.8403	359	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007205.1	s__Ensifer adhaerens_D	77.8391	401	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217095.1	s__Pararhizobium sp003217095	77.8047	355	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	95.84	95.04	0.89	0.86	9	-
GCF_001664485.1	s__Rhizobium sp001664485	77.8013	362	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.08	96.02	0.91	0.83	8	-
GCF_004959855.1	s__SPNT01 sp004959855	77.6777	294	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__SPNT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469595.1	s__Ensifer sp900469595	77.6731	370	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.13	98.13	0.88	0.88	2	-
GCF_000799715.1	s__Rhizobium rhizogenes_C	77.503	300	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001558695.1	s__Paramesorhizobium deserti	77.4639	308	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980555.1	s__Phyllobacterium myrsinacearum	76.8822	200	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.64	98.56	0.99	0.97	5	-
GCA_900539805.1	s__Phyllobacterium sp900539805	76.7847	211	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	96.69	96.69	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:46,748] [INFO] GTDB search result was written to GCF_006516965.1_ASM651696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:46,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:46,757] [INFO] DFAST_QC result json was written to GCF_006516965.1_ASM651696v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:46,758] [INFO] DFAST_QC completed!
[2024-01-24 12:45:46,758] [INFO] Total running time: 0h1m36s