[2024-01-24 11:34:41,295] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f4e2fd8-51c8-4a2a-8849-4bc948625807/dqc_reference
[2024-01-24 11:34:42,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,674] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,675] [INFO] Running command: gunzip -c /var/lib/cwl/stgab5d5d7d-ef78-411c-9007-203596db42af/GCF_016865175.1_ASM1686517v1_genomic.fna.gz | prodigal -d GCF_016865175.1_ASM1686517v1_genomic.fna/cds.fna -a GCF_016865175.1_ASM1686517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:07,451] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:07,451] [INFO] Task started: HMMsearch
[2024-01-24 11:35:07,451] [INFO] Running command: hmmsearch --tblout GCF_016865175.1_ASM1686517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f4e2fd8-51c8-4a2a-8849-4bc948625807/dqc_reference/reference_markers.hmm GCF_016865175.1_ASM1686517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:07,872] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:07,873] [INFO] Found 6/6 markers.
[2024-01-24 11:35:07,947] [INFO] Query marker FASTA was written to GCF_016865175.1_ASM1686517v1_genomic.fna/markers.fasta
[2024-01-24 11:35:07,948] [INFO] Task started: Blastn
[2024-01-24 11:35:07,948] [INFO] Running command: blastn -query GCF_016865175.1_ASM1686517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f4e2fd8-51c8-4a2a-8849-4bc948625807/dqc_reference/reference_markers.fasta -out GCF_016865175.1_ASM1686517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:09,036] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:09,039] [INFO] Selected 24 target genomes.
[2024-01-24 11:35:09,040] [INFO] Target genome list was writen to GCF_016865175.1_ASM1686517v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:09,048] [INFO] Task started: fastANI
[2024-01-24 11:35:09,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgab5d5d7d-ef78-411c-9007-203596db42af/GCF_016865175.1_ASM1686517v1_genomic.fna.gz --refList GCF_016865175.1_ASM1686517v1_genomic.fna/target_genomes.txt --output GCF_016865175.1_ASM1686517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:36,948] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:36,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f4e2fd8-51c8-4a2a-8849-4bc948625807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:36,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f4e2fd8-51c8-4a2a-8849-4bc948625807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:36,966] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:36,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:36,966] [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
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	83.7328	1437	2595	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	81.6004	1053	2595	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	81.564	1090	2595	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	81.5018	1104	2595	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	81.3725	1114	2595	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	81.3518	1069	2595	95	below_threshold
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	81.3426	1139	2595	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	81.3271	1140	2595	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	81.1332	1192	2595	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.779	849	2595	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	80.7465	850	2595	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	80.7159	920	2595	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	80.7052	944	2595	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.5462	838	2595	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	80.5292	936	2595	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	80.4118	811	2595	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	80.3755	832	2595	95	below_threshold
Pararhizobium antarcticum	strain=NAQVI 59	GCA_001885585.1	1798805	1798805	type	True	79.922	827	2595	95	below_threshold
Rhizobium pisi	strain=DSM 30132	GCA_003938655.1	574561	574561	type	True	79.488	803	2595	95	below_threshold
Rhizobium fabae	strain=DSM 19331	GCA_014196235.1	573179	573179	type	True	79.4154	791	2595	95	below_threshold
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	79.3796	783	2595	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.026	594	2595	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.7812	390	2595	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	77.6955	392	2595	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:36,968] [INFO] DFAST Taxonomy check result was written to GCF_016865175.1_ASM1686517v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:36,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:36,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:36,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f4e2fd8-51c8-4a2a-8849-4bc948625807/dqc_reference/checkm_data
[2024-01-24 11:35:36,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:37,042] [INFO] Task started: CheckM
[2024-01-24 11:35:37,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016865175.1_ASM1686517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016865175.1_ASM1686517v1_genomic.fna/checkm_input GCF_016865175.1_ASM1686517v1_genomic.fna/checkm_result
[2024-01-24 11:36:44,103] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:44,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:44,124] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:44,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:44,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016865175.1_ASM1686517v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:44,125] [INFO] Task started: Blastn
[2024-01-24 11:36:44,125] [INFO] Running command: blastn -query GCF_016865175.1_ASM1686517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f4e2fd8-51c8-4a2a-8849-4bc948625807/dqc_reference/reference_markers_gtdb.fasta -out GCF_016865175.1_ASM1686517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:46,093] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:46,096] [INFO] Selected 7 target genomes.
[2024-01-24 11:36:46,096] [INFO] Target genome list was writen to GCF_016865175.1_ASM1686517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:46,117] [INFO] Task started: fastANI
[2024-01-24 11:36:46,117] [INFO] Running command: fastANI --query /var/lib/cwl/stgab5d5d7d-ef78-411c-9007-203596db42af/GCF_016865175.1_ASM1686517v1_genomic.fna.gz --refList GCF_016865175.1_ASM1686517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016865175.1_ASM1686517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:58,926] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:58,933] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:58,933] [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_000583045.1	s__Ensifer adhaerens_A	98.6673	2171	2595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.74	98.60	0.88	0.84	14	conclusive
GCF_001695855.1	s__Ensifer sp001695855	90.3399	1768	2595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.60	98.60	0.94	0.94	3	-
GCF_001270265.1	s__Ensifer adhaerens_B	90.2393	1874	2595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002725.1	s__Ensifer sp002002725	89.1098	1801	2595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.52	98.52	0.94	0.94	2	-
GCF_013371465.1	s__Ensifer sp013371465	88.8091	1762	2595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283195.1	s__Ensifer adhaerens_G	88.6767	1782	2595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.31	98.31	0.94	0.94	2	-
GCA_900469625.1	s__Ensifer sp900469625	87.5252	1673	2595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.94	98.62	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:58,935] [INFO] GTDB search result was written to GCF_016865175.1_ASM1686517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:58,935] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:58,939] [INFO] DFAST_QC result json was written to GCF_016865175.1_ASM1686517v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:58,939] [INFO] DFAST_QC completed!
[2024-01-24 11:36:58,939] [INFO] Total running time: 0h2m18s