[2024-01-24 13:25:58,051] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,054] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,054] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf289186-8022-4e49-a620-d3b67915d7fd/dqc_reference
[2024-01-24 13:26:00,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,377] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg456e3559-2056-42ea-8cef-f35514c9c5fb/GCF_001741865.1_ASM174186v1_genomic.fna.gz | prodigal -d GCF_001741865.1_ASM174186v1_genomic.fna/cds.fna -a GCF_001741865.1_ASM174186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:21,562] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:21,562] [INFO] Task started: HMMsearch
[2024-01-24 13:26:21,562] [INFO] Running command: hmmsearch --tblout GCF_001741865.1_ASM174186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf289186-8022-4e49-a620-d3b67915d7fd/dqc_reference/reference_markers.hmm GCF_001741865.1_ASM174186v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:21,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:21,922] [INFO] Found 6/6 markers.
[2024-01-24 13:26:21,988] [INFO] Query marker FASTA was written to GCF_001741865.1_ASM174186v1_genomic.fna/markers.fasta
[2024-01-24 13:26:21,989] [INFO] Task started: Blastn
[2024-01-24 13:26:21,989] [INFO] Running command: blastn -query GCF_001741865.1_ASM174186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf289186-8022-4e49-a620-d3b67915d7fd/dqc_reference/reference_markers.fasta -out GCF_001741865.1_ASM174186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:23,064] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:23,068] [INFO] Selected 11 target genomes.
[2024-01-24 13:26:23,069] [INFO] Target genome list was writen to GCF_001741865.1_ASM174186v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:23,076] [INFO] Task started: fastANI
[2024-01-24 13:26:23,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg456e3559-2056-42ea-8cef-f35514c9c5fb/GCF_001741865.1_ASM174186v1_genomic.fna.gz --refList GCF_001741865.1_ASM174186v1_genomic.fna/target_genomes.txt --output GCF_001741865.1_ASM174186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:41,759] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:41,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf289186-8022-4e49-a620-d3b67915d7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:41,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf289186-8022-4e49-a620-d3b67915d7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:41,774] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:41,774] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:41,774] [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 vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	100.0	2235	2237	95	conclusive
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	93.3769	1720	2237	95	below_threshold
Bosea lathyri	strain=DSM 26656	GCA_900108245.1	1036778	1036778	type	True	84.3861	1275	2237	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	84.0518	1245	2237	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	83.1957	1103	2237	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	83.1723	1133	2237	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.9427	623	2237	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.9361	650	2237	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	77.8955	397	2237	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.8266	676	2237	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	77.7643	379	2237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:41,776] [INFO] DFAST Taxonomy check result was written to GCF_001741865.1_ASM174186v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:41,777] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:41,777] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:41,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf289186-8022-4e49-a620-d3b67915d7fd/dqc_reference/checkm_data
[2024-01-24 13:26:41,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:41,840] [INFO] Task started: CheckM
[2024-01-24 13:26:41,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001741865.1_ASM174186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001741865.1_ASM174186v1_genomic.fna/checkm_input GCF_001741865.1_ASM174186v1_genomic.fna/checkm_result
[2024-01-24 13:27:43,716] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:43,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:43,747] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:43,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:43,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001741865.1_ASM174186v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:43,750] [INFO] Task started: Blastn
[2024-01-24 13:27:43,750] [INFO] Running command: blastn -query GCF_001741865.1_ASM174186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf289186-8022-4e49-a620-d3b67915d7fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_001741865.1_ASM174186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:45,924] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:46,010] [INFO] Selected 14 target genomes.
[2024-01-24 13:27:46,011] [INFO] Target genome list was writen to GCF_001741865.1_ASM174186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:46,039] [INFO] Task started: fastANI
[2024-01-24 13:27:46,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg456e3559-2056-42ea-8cef-f35514c9c5fb/GCF_001741865.1_ASM174186v1_genomic.fna.gz --refList GCF_001741865.1_ASM174186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001741865.1_ASM174186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:10,474] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:10,492] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:10,492] [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_001741865.1	s__Bosea vaviloviae	100.0	2235	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900113835.1	s__Bosea sp900113835	93.6081	1756	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917105.1	s__Bosea psychrotolerans	93.3786	1720	2237	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	84.7333	1271	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108245.1	s__Bosea lathyri	84.3756	1276	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046175.1	s__Bosea sp003046175	84.1859	1204	2237	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	84.1216	1156	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.00	96.54	0.90	0.82	3	-
GCF_001298265.1	s__Bosea vaviloviae_B	84.1159	1192	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351345.1	s__Bosea caraganae	84.0628	1244	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003241815.1	s__Bosea sp003241815	83.984	1045	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279705.1	s__Bosea sp002279705	83.7727	930	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.41	99.41	0.89	0.89	2	-
GCF_001429395.1	s__Bosea sp001429395	83.5464	1136	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764485.1	s__Bosea sp011764485	83.1353	1110	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248805.1	s__Bosea sp003248805	82.7197	1071	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:10,494] [INFO] GTDB search result was written to GCF_001741865.1_ASM174186v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:10,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:10,499] [INFO] DFAST_QC result json was written to GCF_001741865.1_ASM174186v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:10,500] [INFO] DFAST_QC completed!
[2024-01-24 13:28:10,500] [INFO] Total running time: 0h2m12s