[2024-01-25 18:55:50,694] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:50,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:50,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg0baa4ddc-979c-4156-891f-ded585bf6f5d/dqc_reference
[2024-01-25 18:55:51,876] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:51,877] [INFO] Task started: Prodigal
[2024-01-25 18:55:51,877] [INFO] Running command: gunzip -c /var/lib/cwl/stg269768c8-76e6-4dab-9772-42a06c43dc06/GCF_014764685.1_ASM1476468v1_genomic.fna.gz | prodigal -d GCF_014764685.1_ASM1476468v1_genomic.fna/cds.fna -a GCF_014764685.1_ASM1476468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:06,271] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:06,272] [INFO] Task started: HMMsearch
[2024-01-25 18:56:06,272] [INFO] Running command: hmmsearch --tblout GCF_014764685.1_ASM1476468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0baa4ddc-979c-4156-891f-ded585bf6f5d/dqc_reference/reference_markers.hmm GCF_014764685.1_ASM1476468v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:06,557] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:06,558] [INFO] Found 6/6 markers.
[2024-01-25 18:56:06,609] [INFO] Query marker FASTA was written to GCF_014764685.1_ASM1476468v1_genomic.fna/markers.fasta
[2024-01-25 18:56:06,610] [INFO] Task started: Blastn
[2024-01-25 18:56:06,610] [INFO] Running command: blastn -query GCF_014764685.1_ASM1476468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0baa4ddc-979c-4156-891f-ded585bf6f5d/dqc_reference/reference_markers.fasta -out GCF_014764685.1_ASM1476468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:07,697] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:07,700] [INFO] Selected 11 target genomes.
[2024-01-25 18:56:07,700] [INFO] Target genome list was writen to GCF_014764685.1_ASM1476468v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:07,711] [INFO] Task started: fastANI
[2024-01-25 18:56:07,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg269768c8-76e6-4dab-9772-42a06c43dc06/GCF_014764685.1_ASM1476468v1_genomic.fna.gz --refList GCF_014764685.1_ASM1476468v1_genomic.fna/target_genomes.txt --output GCF_014764685.1_ASM1476468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:22,116] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:22,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0baa4ddc-979c-4156-891f-ded585bf6f5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:22,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0baa4ddc-979c-4156-891f-ded585bf6f5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:22,125] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:56:22,125] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:56:22,125] [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 robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	86.7308	1190	1943	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	86.6782	1178	1943	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	83.8381	1097	1943	95	below_threshold
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	83.5203	1162	1943	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	83.2985	1178	1943	95	below_threshold
Bosea lathyri	strain=DSM 26656	GCA_900108245.1	1036778	1036778	type	True	83.0969	1086	1943	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.3142	691	1943	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	78.2793	402	1943	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	78.2781	428	1943	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	77.9395	381	1943	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.7532	600	1943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:22,127] [INFO] DFAST Taxonomy check result was written to GCF_014764685.1_ASM1476468v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:22,127] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:22,128] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:22,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0baa4ddc-979c-4156-891f-ded585bf6f5d/dqc_reference/checkm_data
[2024-01-25 18:56:22,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:22,184] [INFO] Task started: CheckM
[2024-01-25 18:56:22,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014764685.1_ASM1476468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014764685.1_ASM1476468v1_genomic.fna/checkm_input GCF_014764685.1_ASM1476468v1_genomic.fna/checkm_result
[2024-01-25 18:57:08,349] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:08,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:08,368] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:08,368] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:08,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014764685.1_ASM1476468v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:08,369] [INFO] Task started: Blastn
[2024-01-25 18:57:08,369] [INFO] Running command: blastn -query GCF_014764685.1_ASM1476468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0baa4ddc-979c-4156-891f-ded585bf6f5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014764685.1_ASM1476468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:10,620] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:10,623] [INFO] Selected 12 target genomes.
[2024-01-25 18:57:10,624] [INFO] Target genome list was writen to GCF_014764685.1_ASM1476468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:10,641] [INFO] Task started: fastANI
[2024-01-25 18:57:10,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg269768c8-76e6-4dab-9772-42a06c43dc06/GCF_014764685.1_ASM1476468v1_genomic.fna.gz --refList GCF_014764685.1_ASM1476468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014764685.1_ASM1476468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:27,410] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:27,418] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:27,418] [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_000745475.1	s__Bosea vestrisii	98.0155	1616	1943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	98.16	98.02	0.92	0.87	6	conclusive
GCA_900466745.1	s__Bosea sp900466745	88.2964	1081	1943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_002220095.1	s__Bosea sp002220095	88.0373	1341	1943	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	87.3241	1232	1943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.21	98.43	0.96	0.93	3	-
GCF_016428755.1	s__Bosea sp016428755	87.1022	1197	1943	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	86.7121	1174	1943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.77	99.77	0.94	0.94	2	-
GCF_900102525.1	s__Bosea robiniae	86.706	1193	1943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.62	97.45	0.92	0.88	4	-
GCF_008253865.1	s__Bosea sp008253865	86.5867	1328	1943	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	86.5753	1163	1943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308015.1	s__Bosea sp017308015	85.9401	1068	1943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144595.1	s__Bosea sp004144595	85.9041	1040	1943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473415.1	s__Bosea sp900473415	85.6552	1124	1943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:27,420] [INFO] GTDB search result was written to GCF_014764685.1_ASM1476468v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:27,421] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:27,424] [INFO] DFAST_QC result json was written to GCF_014764685.1_ASM1476468v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:27,424] [INFO] DFAST_QC completed!
[2024-01-25 18:57:27,424] [INFO] Total running time: 0h1m37s