[2024-01-24 14:06:18,006] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:18,008] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:18,008] [INFO] DQC Reference Directory: /var/lib/cwl/stg40fe9336-ff57-4e8c-8226-f9be6fa1f782/dqc_reference
[2024-01-24 14:06:19,370] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:19,371] [INFO] Task started: Prodigal
[2024-01-24 14:06:19,371] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1a2b5fd-345c-4dcf-8380-9417c0192897/GCF_003351345.1_ASM335134v1_genomic.fna.gz | prodigal -d GCF_003351345.1_ASM335134v1_genomic.fna/cds.fna -a GCF_003351345.1_ASM335134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:37,707] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:37,707] [INFO] Task started: HMMsearch
[2024-01-24 14:06:37,708] [INFO] Running command: hmmsearch --tblout GCF_003351345.1_ASM335134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40fe9336-ff57-4e8c-8226-f9be6fa1f782/dqc_reference/reference_markers.hmm GCF_003351345.1_ASM335134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:38,124] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:38,125] [INFO] Found 6/6 markers.
[2024-01-24 14:06:38,179] [INFO] Query marker FASTA was written to GCF_003351345.1_ASM335134v1_genomic.fna/markers.fasta
[2024-01-24 14:06:38,180] [INFO] Task started: Blastn
[2024-01-24 14:06:38,180] [INFO] Running command: blastn -query GCF_003351345.1_ASM335134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40fe9336-ff57-4e8c-8226-f9be6fa1f782/dqc_reference/reference_markers.fasta -out GCF_003351345.1_ASM335134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:39,329] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:39,332] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:39,333] [INFO] Target genome list was writen to GCF_003351345.1_ASM335134v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:39,337] [INFO] Task started: fastANI
[2024-01-24 14:06:39,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1a2b5fd-345c-4dcf-8380-9417c0192897/GCF_003351345.1_ASM335134v1_genomic.fna.gz --refList GCF_003351345.1_ASM335134v1_genomic.fna/target_genomes.txt --output GCF_003351345.1_ASM335134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:59,828] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:59,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40fe9336-ff57-4e8c-8226-f9be6fa1f782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:59,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40fe9336-ff57-4e8c-8226-f9be6fa1f782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:59,839] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:59,839] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:59,840] [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
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	100.0	2034	2035	95	conclusive
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	84.1216	1212	2035	95	below_threshold
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	84.0736	1168	2035	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	83.9054	1084	2035	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	83.8101	1048	2035	95	below_threshold
Bosea lathyri	strain=DSM 26656	GCA_900108245.1	1036778	1036778	type	True	83.6746	1142	2035	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.6872	710	2035	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.5481	715	2035	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	78.456	689	2035	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	78.3068	558	2035	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	78.1422	570	2035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:59,841] [INFO] DFAST Taxonomy check result was written to GCF_003351345.1_ASM335134v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:59,842] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:59,842] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:59,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40fe9336-ff57-4e8c-8226-f9be6fa1f782/dqc_reference/checkm_data
[2024-01-24 14:06:59,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:59,900] [INFO] Task started: CheckM
[2024-01-24 14:06:59,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003351345.1_ASM335134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003351345.1_ASM335134v1_genomic.fna/checkm_input GCF_003351345.1_ASM335134v1_genomic.fna/checkm_result
[2024-01-24 14:07:50,784] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:50,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:50,808] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:50,808] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:50,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003351345.1_ASM335134v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:50,809] [INFO] Task started: Blastn
[2024-01-24 14:07:50,809] [INFO] Running command: blastn -query GCF_003351345.1_ASM335134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40fe9336-ff57-4e8c-8226-f9be6fa1f782/dqc_reference/reference_markers_gtdb.fasta -out GCF_003351345.1_ASM335134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:53,055] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:53,060] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:53,060] [INFO] Target genome list was writen to GCF_003351345.1_ASM335134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:53,101] [INFO] Task started: fastANI
[2024-01-24 14:07:53,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1a2b5fd-345c-4dcf-8380-9417c0192897/GCF_003351345.1_ASM335134v1_genomic.fna.gz --refList GCF_003351345.1_ASM335134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003351345.1_ASM335134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:23,718] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:23,734] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:23,734] [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_003351345.1	s__Bosea caraganae	100.0	2034	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004341515.1	s__Bosea sp004341515	88.312	1541	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185715.1	s__Bosea sp900185715	84.3505	1093	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470775.1	s__Bosea sp900470775	84.1748	1138	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713455.1	s__Bosea sp001713455	84.0547	1085	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.00	96.54	0.90	0.82	3	-
GCF_004123845.1	s__Bosea sp004123845	83.9844	1178	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168195.1	s__Bosea thiooxidans	83.9252	1082	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.77	99.77	0.94	0.94	2	-
GCF_016428755.1	s__Bosea sp016428755	83.841	1037	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308075.1	s__Bosea sp017308075	83.8255	1095	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.81	97.81	0.86	0.86	2	-
GCF_011764485.1	s__Bosea sp011764485	83.7826	1060	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873125.1	s__Bosea sp014873125	83.777	1091	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001556125.1	s__Bosea sp001556125	83.7611	1018	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	96.92	96.82	0.82	0.77	9	-
GCF_001509835.1	s__Bosea sp001509835	83.7455	1180	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003952665.1	s__Bosea sp003952665	83.6273	1226	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000735605.1	s__Bosea sp000735605	83.5392	1150	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001748145.1	s__Bosea sp001748145	83.2617	1188	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470095.1	s__Bosea sp900470095	83.2518	1151	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426225.1	s__Bosea sp001426225	83.2431	985	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898115.1	s__Bosea sp001898115	83.1132	1010	2035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.21	98.43	0.96	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:23,737] [INFO] GTDB search result was written to GCF_003351345.1_ASM335134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:23,738] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:23,744] [INFO] DFAST_QC result json was written to GCF_003351345.1_ASM335134v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:23,745] [INFO] DFAST_QC completed!
[2024-01-24 14:08:23,745] [INFO] Total running time: 0h2m6s