[2024-01-25 20:05:35,591] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:35,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:35,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg650e4886-8b6c-47e3-8b83-ef95b939e60c/dqc_reference
[2024-01-25 20:05:36,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:36,719] [INFO] Task started: Prodigal
[2024-01-25 20:05:36,719] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b621808-c0f0-459e-abc2-feaf7c072766/GCF_010500815.1_ASM1050081v1_genomic.fna.gz | prodigal -d GCF_010500815.1_ASM1050081v1_genomic.fna/cds.fna -a GCF_010500815.1_ASM1050081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:50,523] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:50,523] [INFO] Task started: HMMsearch
[2024-01-25 20:05:50,523] [INFO] Running command: hmmsearch --tblout GCF_010500815.1_ASM1050081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg650e4886-8b6c-47e3-8b83-ef95b939e60c/dqc_reference/reference_markers.hmm GCF_010500815.1_ASM1050081v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:50,850] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:50,851] [INFO] Found 6/6 markers.
[2024-01-25 20:05:50,907] [INFO] Query marker FASTA was written to GCF_010500815.1_ASM1050081v1_genomic.fna/markers.fasta
[2024-01-25 20:05:50,908] [INFO] Task started: Blastn
[2024-01-25 20:05:50,908] [INFO] Running command: blastn -query GCF_010500815.1_ASM1050081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg650e4886-8b6c-47e3-8b83-ef95b939e60c/dqc_reference/reference_markers.fasta -out GCF_010500815.1_ASM1050081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:51,971] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:51,974] [INFO] Selected 14 target genomes.
[2024-01-25 20:05:51,974] [INFO] Target genome list was writen to GCF_010500815.1_ASM1050081v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:51,984] [INFO] Task started: fastANI
[2024-01-25 20:05:51,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b621808-c0f0-459e-abc2-feaf7c072766/GCF_010500815.1_ASM1050081v1_genomic.fna.gz --refList GCF_010500815.1_ASM1050081v1_genomic.fna/target_genomes.txt --output GCF_010500815.1_ASM1050081v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:06,991] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:06,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg650e4886-8b6c-47e3-8b83-ef95b939e60c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:06,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg650e4886-8b6c-47e3-8b83-ef95b939e60c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:07,001] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:06:07,001] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:07,001] [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
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	100.0	1887	1889	95	conclusive
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	84.3464	1173	1889	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	84.2394	1191	1889	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	80.7809	778	1889	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	80.7796	810	1889	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	80.7307	798	1889	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.7195	802	1889	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	80.7168	805	1889	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.7118	811	1889	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	79.7204	631	1889	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	78.7532	579	1889	95	below_threshold
Fulvimarina pelagi	strain=HTCC2506	GCA_000153705.1	217511	217511	type	True	78.4492	439	1889	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.0672	453	1889	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.0258	489	1889	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:07,002] [INFO] DFAST Taxonomy check result was written to GCF_010500815.1_ASM1050081v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:07,003] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:07,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:07,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg650e4886-8b6c-47e3-8b83-ef95b939e60c/dqc_reference/checkm_data
[2024-01-25 20:06:07,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:07,065] [INFO] Task started: CheckM
[2024-01-25 20:06:07,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010500815.1_ASM1050081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010500815.1_ASM1050081v1_genomic.fna/checkm_input GCF_010500815.1_ASM1050081v1_genomic.fna/checkm_result
[2024-01-25 20:06:50,554] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:50,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:50,573] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:50,573] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:50,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010500815.1_ASM1050081v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:50,573] [INFO] Task started: Blastn
[2024-01-25 20:06:50,574] [INFO] Running command: blastn -query GCF_010500815.1_ASM1050081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg650e4886-8b6c-47e3-8b83-ef95b939e60c/dqc_reference/reference_markers_gtdb.fasta -out GCF_010500815.1_ASM1050081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:52,766] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:52,769] [INFO] Selected 7 target genomes.
[2024-01-25 20:06:52,769] [INFO] Target genome list was writen to GCF_010500815.1_ASM1050081v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:52,776] [INFO] Task started: fastANI
[2024-01-25 20:06:52,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b621808-c0f0-459e-abc2-feaf7c072766/GCF_010500815.1_ASM1050081v1_genomic.fna.gz --refList GCF_010500815.1_ASM1050081v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010500815.1_ASM1050081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:02,420] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:02,426] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:02,426] [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_010500815.1	s__Jiella pacifica	100.0	1887	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002088275.1	s__Jiella sp002088275	85.989	1290	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	85.7917	1239	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	84.3217	1177	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	84.2406	1191	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	83.664	1102	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349315.1	s__Jiella sp017349315	81.5177	894	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:02,431] [INFO] GTDB search result was written to GCF_010500815.1_ASM1050081v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:02,432] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:02,434] [INFO] DFAST_QC result json was written to GCF_010500815.1_ASM1050081v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:02,435] [INFO] DFAST_QC completed!
[2024-01-25 20:07:02,435] [INFO] Total running time: 0h1m27s