[2024-01-24 12:14:33,763] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,764] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaf1a0c7-6d5d-41d1-8398-807c02dc90a3/dqc_reference
[2024-01-24 12:14:35,227] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,227] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,228] [INFO] Running command: gunzip -c /var/lib/cwl/stg4da0b02d-436d-4bc8-9106-eec29144aa84/GCF_022968135.1_ASM2296813v1_genomic.fna.gz | prodigal -d GCF_022968135.1_ASM2296813v1_genomic.fna/cds.fna -a GCF_022968135.1_ASM2296813v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:47,810] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:47,810] [INFO] Task started: HMMsearch
[2024-01-24 12:14:47,810] [INFO] Running command: hmmsearch --tblout GCF_022968135.1_ASM2296813v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaf1a0c7-6d5d-41d1-8398-807c02dc90a3/dqc_reference/reference_markers.hmm GCF_022968135.1_ASM2296813v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:48,059] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:48,060] [INFO] Found 6/6 markers.
[2024-01-24 12:14:48,102] [INFO] Query marker FASTA was written to GCF_022968135.1_ASM2296813v1_genomic.fna/markers.fasta
[2024-01-24 12:14:48,102] [INFO] Task started: Blastn
[2024-01-24 12:14:48,102] [INFO] Running command: blastn -query GCF_022968135.1_ASM2296813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaf1a0c7-6d5d-41d1-8398-807c02dc90a3/dqc_reference/reference_markers.fasta -out GCF_022968135.1_ASM2296813v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:49,076] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:49,079] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:49,079] [INFO] Target genome list was writen to GCF_022968135.1_ASM2296813v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:49,084] [INFO] Task started: fastANI
[2024-01-24 12:14:49,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg4da0b02d-436d-4bc8-9106-eec29144aa84/GCF_022968135.1_ASM2296813v1_genomic.fna.gz --refList GCF_022968135.1_ASM2296813v1_genomic.fna/target_genomes.txt --output GCF_022968135.1_ASM2296813v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:08,130] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:08,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaf1a0c7-6d5d-41d1-8398-807c02dc90a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:08,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaf1a0c7-6d5d-41d1-8398-807c02dc90a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:08,142] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:08,142] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:08,143] [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
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	81.8008	832	1593	95	below_threshold
Pseudorhizobium flavum	strain=DSM 102134	GCA_014201495.1	1335061	1335061	type	True	81.659	826	1593	95	below_threshold
Pseudorhizobium halotolerans	strain=AB21	GCA_902153235.3	1233081	1233081	type	True	81.6462	837	1593	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_902502825.2	1335061	1335061	type	True	81.596	834	1593	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	81.5425	822	1593	95	below_threshold
Pseudorhizobium endolithicum	strain=JC140	GCA_902153245.3	1191678	1191678	type	True	81.5103	859	1593	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	79.8399	702	1593	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.6113	639	1593	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.4168	587	1593	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.4009	590	1593	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	79.3882	572	1593	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	79.3726	627	1593	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	79.3516	607	1593	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.3044	534	1593	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.2301	519	1593	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	79.0449	522	1593	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	78.9358	551	1593	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	78.8925	542	1593	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	78.8388	541	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:08,144] [INFO] DFAST Taxonomy check result was written to GCF_022968135.1_ASM2296813v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:08,144] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:08,144] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:08,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaf1a0c7-6d5d-41d1-8398-807c02dc90a3/dqc_reference/checkm_data
[2024-01-24 12:15:08,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:08,190] [INFO] Task started: CheckM
[2024-01-24 12:15:08,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022968135.1_ASM2296813v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022968135.1_ASM2296813v1_genomic.fna/checkm_input GCF_022968135.1_ASM2296813v1_genomic.fna/checkm_result
[2024-01-24 12:15:45,092] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:45,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:45,107] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:45,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:45,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022968135.1_ASM2296813v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:45,107] [INFO] Task started: Blastn
[2024-01-24 12:15:45,107] [INFO] Running command: blastn -query GCF_022968135.1_ASM2296813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaf1a0c7-6d5d-41d1-8398-807c02dc90a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_022968135.1_ASM2296813v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:47,085] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:47,089] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:47,089] [INFO] Target genome list was writen to GCF_022968135.1_ASM2296813v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:47,099] [INFO] Task started: fastANI
[2024-01-24 12:15:47,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg4da0b02d-436d-4bc8-9106-eec29144aa84/GCF_022968135.1_ASM2296813v1_genomic.fna.gz --refList GCF_022968135.1_ASM2296813v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022968135.1_ASM2296813v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:12,435] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:12,448] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:12,448] [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
GCA_000722615.1	s__Pseudorhizobium pelagicum	82.0519	976	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	97.63	97.12	0.87	0.82	8	-
GCF_902502825.2	s__Pseudorhizobium flavum	81.6029	833	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	96.75	95.31	0.86	0.77	9	-
GCF_902153245.2	s__Pseudorhizobium endolithicum	81.508	859	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	98.09	98.09	0.93	0.93	2	-
GCF_000732195.1	s__Neorhizobium vignae	79.8355	703	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282095.2	s__Neorhizobium sp000282095	79.7878	731	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877055.1	s__Neorhizobium galegae_D	79.709	721	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111905.1	s__Neorhizobium sp900111905	79.6221	686	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968635.1	s__Neorhizobium alkalisoli	79.6156	638	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469955.1	s__Neorhizobium sp900469955	79.5833	627	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796995.1	s__Allorhizobium sp002796995	79.5086	617	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
GCF_900492205.1	s__Allorhizobium naphthalenivorans_A	79.4539	576	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.27	95.27	0.88	0.88	2	-
GCF_002968575.1	s__Neorhizobium huautlense	79.3919	624	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCA_900469445.1	s__Neorhizobium sp900469445	79.2264	596	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	99.00	97.21	0.95	0.90	4	-
GCF_001429285.1	s__Ensifer sp001429285	79.1605	501	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.69	95.18	0.90	0.85	16	-
GCF_002007205.1	s__Ensifer adhaerens_D	79.0673	542	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940685.1	s__Ensifer adhaerens_E	78.9902	555	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172795.2	s__Rhizobium sp000172795	78.9898	539	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919405.1	s__Ensifer sp000799055	78.9672	546	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.37	96.05	0.91	0.88	3	-
GCF_004343585.1	s__Neorhizobium sp004343585	78.9585	548	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651855.1	s__Sinorhizobium americanum	78.861	475	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.81	98.12	0.92	0.85	4	-
GCF_001662075.1	s__Rhizobium bangladeshense_B	78.8437	543	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:12,449] [INFO] GTDB search result was written to GCF_022968135.1_ASM2296813v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:12,450] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:12,454] [INFO] DFAST_QC result json was written to GCF_022968135.1_ASM2296813v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:12,454] [INFO] DFAST_QC completed!
[2024-01-24 12:16:12,454] [INFO] Total running time: 0h1m39s