[2024-01-24 13:40:28,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0cb8a59-417d-468b-b6cb-a37fd1dfb06b/dqc_reference
[2024-01-24 13:40:31,141] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,142] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,142] [INFO] Running command: gunzip -c /var/lib/cwl/stgd75b3693-3adc-46e4-9bf2-9d83a21dccb9/GCF_011603255.1_ASM1160325v1_genomic.fna.gz | prodigal -d GCF_011603255.1_ASM1160325v1_genomic.fna/cds.fna -a GCF_011603255.1_ASM1160325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:47,560] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:47,560] [INFO] Task started: HMMsearch
[2024-01-24 13:40:47,560] [INFO] Running command: hmmsearch --tblout GCF_011603255.1_ASM1160325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0cb8a59-417d-468b-b6cb-a37fd1dfb06b/dqc_reference/reference_markers.hmm GCF_011603255.1_ASM1160325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:47,913] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:47,915] [INFO] Found 6/6 markers.
[2024-01-24 13:40:47,970] [INFO] Query marker FASTA was written to GCF_011603255.1_ASM1160325v1_genomic.fna/markers.fasta
[2024-01-24 13:40:47,970] [INFO] Task started: Blastn
[2024-01-24 13:40:47,970] [INFO] Running command: blastn -query GCF_011603255.1_ASM1160325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0cb8a59-417d-468b-b6cb-a37fd1dfb06b/dqc_reference/reference_markers.fasta -out GCF_011603255.1_ASM1160325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:49,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:49,043] [INFO] Selected 20 target genomes.
[2024-01-24 13:40:49,043] [INFO] Target genome list was writen to GCF_011603255.1_ASM1160325v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:49,056] [INFO] Task started: fastANI
[2024-01-24 13:40:49,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgd75b3693-3adc-46e4-9bf2-9d83a21dccb9/GCF_011603255.1_ASM1160325v1_genomic.fna.gz --refList GCF_011603255.1_ASM1160325v1_genomic.fna/target_genomes.txt --output GCF_011603255.1_ASM1160325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:14,875] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:14,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0cb8a59-417d-468b-b6cb-a37fd1dfb06b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:14,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0cb8a59-417d-468b-b6cb-a37fd1dfb06b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:14,901] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:14,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:14,902] [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
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	80.4567	704	1810	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.4362	726	1810	95	below_threshold
Rhizobium giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	80.2673	810	1810	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.1855	805	1810	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	80.1794	701	1810	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	80.1768	692	1810	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	80.1619	731	1810	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	80.1182	815	1810	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	80.1084	728	1810	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.0569	722	1810	95	below_threshold
Pararhizobium antarcticum	strain=NAQVI 59	GCA_001885585.1	1798805	1798805	type	True	79.8847	771	1810	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	79.8578	711	1810	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	79.8357	747	1810	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	79.5044	717	1810	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	79.471	628	1810	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	79.4138	651	1810	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	79.1571	636	1810	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	78.9863	642	1810	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	78.843	531	1810	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	78.7777	612	1810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,905] [INFO] DFAST Taxonomy check result was written to GCF_011603255.1_ASM1160325v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:14,905] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:14,906] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:14,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0cb8a59-417d-468b-b6cb-a37fd1dfb06b/dqc_reference/checkm_data
[2024-01-24 13:41:14,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:14,964] [INFO] Task started: CheckM
[2024-01-24 13:41:14,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011603255.1_ASM1160325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011603255.1_ASM1160325v1_genomic.fna/checkm_input GCF_011603255.1_ASM1160325v1_genomic.fna/checkm_result
[2024-01-24 13:42:05,710] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:05,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:05,739] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:05,740] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:05,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011603255.1_ASM1160325v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:05,740] [INFO] Task started: Blastn
[2024-01-24 13:42:05,741] [INFO] Running command: blastn -query GCF_011603255.1_ASM1160325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0cb8a59-417d-468b-b6cb-a37fd1dfb06b/dqc_reference/reference_markers_gtdb.fasta -out GCF_011603255.1_ASM1160325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:07,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:07,776] [INFO] Selected 5 target genomes.
[2024-01-24 13:42:07,776] [INFO] Target genome list was writen to GCF_011603255.1_ASM1160325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:07,786] [INFO] Task started: fastANI
[2024-01-24 13:42:07,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgd75b3693-3adc-46e4-9bf2-9d83a21dccb9/GCF_011603255.1_ASM1160325v1_genomic.fna.gz --refList GCF_011603255.1_ASM1160325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011603255.1_ASM1160325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:15,401] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:15,410] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:15,410] [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_003217095.1	s__Pararhizobium sp003217095	95.0472	1528	1810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	95.84	95.04	0.89	0.86	9	conclusive
GCF_900067135.1	s__Pararhizobium sp900067135	92.6158	1434	1810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900467185.1	s__Pararhizobium sp900467185	91.671	1460	1810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111275.1	s__Pararhizobium sp900111275	88.7928	1387	1810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424045.1	s__Pararhizobium sp001424045	88.0302	1325	1810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	97.68	97.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,411] [INFO] GTDB search result was written to GCF_011603255.1_ASM1160325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:15,412] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:15,415] [INFO] DFAST_QC result json was written to GCF_011603255.1_ASM1160325v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:15,416] [INFO] DFAST_QC completed!
[2024-01-24 13:42:15,416] [INFO] Total running time: 0h1m47s