[2024-01-24 13:55:20,195] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:20,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:20,202] [INFO] DQC Reference Directory: /var/lib/cwl/stga8c24204-73bc-423f-9fb7-4fdfaee9b8cd/dqc_reference
[2024-01-24 13:55:21,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,568] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,569] [INFO] Running command: gunzip -c /var/lib/cwl/stg70ff362f-365a-413a-8ad2-80e596b61287/GCF_014201355.1_ASM1420135v1_genomic.fna.gz | prodigal -d GCF_014201355.1_ASM1420135v1_genomic.fna/cds.fna -a GCF_014201355.1_ASM1420135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:41,950] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:41,950] [INFO] Task started: HMMsearch
[2024-01-24 13:55:41,950] [INFO] Running command: hmmsearch --tblout GCF_014201355.1_ASM1420135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8c24204-73bc-423f-9fb7-4fdfaee9b8cd/dqc_reference/reference_markers.hmm GCF_014201355.1_ASM1420135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:42,363] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:42,365] [INFO] Found 6/6 markers.
[2024-01-24 13:55:42,428] [INFO] Query marker FASTA was written to GCF_014201355.1_ASM1420135v1_genomic.fna/markers.fasta
[2024-01-24 13:55:42,429] [INFO] Task started: Blastn
[2024-01-24 13:55:42,429] [INFO] Running command: blastn -query GCF_014201355.1_ASM1420135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c24204-73bc-423f-9fb7-4fdfaee9b8cd/dqc_reference/reference_markers.fasta -out GCF_014201355.1_ASM1420135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:43,493] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:43,496] [INFO] Selected 14 target genomes.
[2024-01-24 13:55:43,496] [INFO] Target genome list was writen to GCF_014201355.1_ASM1420135v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:43,508] [INFO] Task started: fastANI
[2024-01-24 13:55:43,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ff362f-365a-413a-8ad2-80e596b61287/GCF_014201355.1_ASM1420135v1_genomic.fna.gz --refList GCF_014201355.1_ASM1420135v1_genomic.fna/target_genomes.txt --output GCF_014201355.1_ASM1420135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:01,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:01,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8c24204-73bc-423f-9fb7-4fdfaee9b8cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:01,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8c24204-73bc-423f-9fb7-4fdfaee9b8cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:01,242] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:01,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:01,243] [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
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	100.0	2133	2134	95	conclusive
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	99.9975	2128	2134	95	conclusive
Rhizobium smilacinae	strain=PTYR-5	GCA_006335145.1	1395944	1395944	type	True	85.657	1490	2134	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	80.8135	952	2134	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	80.7495	916	2134	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.9706	799	2134	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	79.6233	758	2134	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.3509	722	2134	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.2254	650	2134	95	below_threshold
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	79.1596	550	2134	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.1505	578	2134	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	79.0458	555	2134	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.0267	680	2134	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	79.0138	632	2134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:01,245] [INFO] DFAST Taxonomy check result was written to GCF_014201355.1_ASM1420135v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:01,246] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:01,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:01,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8c24204-73bc-423f-9fb7-4fdfaee9b8cd/dqc_reference/checkm_data
[2024-01-24 13:56:01,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:01,320] [INFO] Task started: CheckM
[2024-01-24 13:56:01,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201355.1_ASM1420135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201355.1_ASM1420135v1_genomic.fna/checkm_input GCF_014201355.1_ASM1420135v1_genomic.fna/checkm_result
[2024-01-24 13:56:57,899] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:57,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:57,918] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:57,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:57,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201355.1_ASM1420135v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:57,920] [INFO] Task started: Blastn
[2024-01-24 13:56:57,920] [INFO] Running command: blastn -query GCF_014201355.1_ASM1420135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c24204-73bc-423f-9fb7-4fdfaee9b8cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201355.1_ASM1420135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:00,053] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:00,058] [INFO] Selected 8 target genomes.
[2024-01-24 13:57:00,058] [INFO] Target genome list was writen to GCF_014201355.1_ASM1420135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:00,078] [INFO] Task started: fastANI
[2024-01-24 13:57:00,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ff362f-365a-413a-8ad2-80e596b61287/GCF_014201355.1_ASM1420135v1_genomic.fna.gz --refList GCF_014201355.1_ASM1420135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201355.1_ASM1420135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:11,846] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:11,856] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:11,857] [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_014201355.1	s__Neorhizobium wenxiniae	100.0	2133	2134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.63	97.27	0.93	0.87	3	conclusive
GCA_900472575.1	s__Neorhizobium cellulosilyticum	92.3116	1681	2134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.58	97.10	0.87	0.85	7	-
GCA_002500765.1	s__Neorhizobium sp002500765	87.6703	1137	2134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376235.1	s__Neorhizobium sp002376235	87.5232	1416	2134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469445.1	s__Neorhizobium sp900469445	87.1189	1467	2134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	99.00	97.21	0.95	0.90	4	-
GCA_900466875.1	s__Neorhizobium sp900466875	86.544	1422	2134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335145.1	s__Neorhizobium smilacinae	85.648	1491	2134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003597675.1	s__Neorhizobium sp003597675	83.3263	1205	2134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:11,858] [INFO] GTDB search result was written to GCF_014201355.1_ASM1420135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:11,859] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:11,862] [INFO] DFAST_QC result json was written to GCF_014201355.1_ASM1420135v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:11,863] [INFO] DFAST_QC completed!
[2024-01-24 13:57:11,863] [INFO] Total running time: 0h1m52s