[2024-01-24 15:02:37,188] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:37,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:37,191] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5557d05-efc8-41b7-b5a8-de3d21e81253/dqc_reference
[2024-01-24 15:02:38,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,645] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,645] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdf14534-7050-449b-b397-a6805673ef4a/GCF_002930645.1_ASM293064v1_genomic.fna.gz | prodigal -d GCF_002930645.1_ASM293064v1_genomic.fna/cds.fna -a GCF_002930645.1_ASM293064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:52,559] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:52,559] [INFO] Task started: HMMsearch
[2024-01-24 15:02:52,559] [INFO] Running command: hmmsearch --tblout GCF_002930645.1_ASM293064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5557d05-efc8-41b7-b5a8-de3d21e81253/dqc_reference/reference_markers.hmm GCF_002930645.1_ASM293064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:52,902] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:52,903] [INFO] Found 6/6 markers.
[2024-01-24 15:02:52,947] [INFO] Query marker FASTA was written to GCF_002930645.1_ASM293064v1_genomic.fna/markers.fasta
[2024-01-24 15:02:52,948] [INFO] Task started: Blastn
[2024-01-24 15:02:52,948] [INFO] Running command: blastn -query GCF_002930645.1_ASM293064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5557d05-efc8-41b7-b5a8-de3d21e81253/dqc_reference/reference_markers.fasta -out GCF_002930645.1_ASM293064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:54,075] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:54,078] [INFO] Selected 14 target genomes.
[2024-01-24 15:02:54,078] [INFO] Target genome list was writen to GCF_002930645.1_ASM293064v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:54,122] [INFO] Task started: fastANI
[2024-01-24 15:02:54,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf14534-7050-449b-b397-a6805673ef4a/GCF_002930645.1_ASM293064v1_genomic.fna.gz --refList GCF_002930645.1_ASM293064v1_genomic.fna/target_genomes.txt --output GCF_002930645.1_ASM293064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:07,871] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:07,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5557d05-efc8-41b7-b5a8-de3d21e81253/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:07,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5557d05-efc8-41b7-b5a8-de3d21e81253/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:07,884] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:07,884] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:07,885] [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
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	100.0	1540	1542	95	conclusive
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	80.2042	677	1542	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	80.0613	656	1542	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	79.9301	627	1542	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	79.9226	686	1542	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	79.026	526	1542	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	78.931	566	1542	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004799025.1	381431	381431	type	True	78.823	520	1542	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	78.8093	519	1542	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	78.0347	375	1542	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.2019	243	1542	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.0236	332	1542	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.9182	244	1542	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.5532	234	1542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:07,887] [INFO] DFAST Taxonomy check result was written to GCF_002930645.1_ASM293064v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:07,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:07,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:07,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5557d05-efc8-41b7-b5a8-de3d21e81253/dqc_reference/checkm_data
[2024-01-24 15:03:07,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:07,935] [INFO] Task started: CheckM
[2024-01-24 15:03:07,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002930645.1_ASM293064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002930645.1_ASM293064v1_genomic.fna/checkm_input GCF_002930645.1_ASM293064v1_genomic.fna/checkm_result
[2024-01-24 15:03:55,231] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:55,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:55,252] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:55,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:55,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002930645.1_ASM293064v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:55,253] [INFO] Task started: Blastn
[2024-01-24 15:03:55,253] [INFO] Running command: blastn -query GCF_002930645.1_ASM293064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5557d05-efc8-41b7-b5a8-de3d21e81253/dqc_reference/reference_markers_gtdb.fasta -out GCF_002930645.1_ASM293064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:57,260] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:57,265] [INFO] Selected 11 target genomes.
[2024-01-24 15:03:57,265] [INFO] Target genome list was writen to GCF_002930645.1_ASM293064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:57,273] [INFO] Task started: fastANI
[2024-01-24 15:03:57,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf14534-7050-449b-b397-a6805673ef4a/GCF_002930645.1_ASM293064v1_genomic.fna.gz --refList GCF_002930645.1_ASM293064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002930645.1_ASM293064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:09,511] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:09,526] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:09,526] [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_002930645.1	s__Solimonas_A fluminis	100.0	1540	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003428335.1	s__Solimonas_A sp003428335	87.8783	1181	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	80.3241	596	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	80.2105	676	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	80.0837	653	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	80.0424	688	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	79.9589	681	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	79.8997	630	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730135.1	s__Stagnimonas aquatica	79.6324	600	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364935.1	s__Panacagrimonas perspica	78.8632	512	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Panacagrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903970595.1	s__Nevskia sp903970595	78.6123	461	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:09,538] [INFO] GTDB search result was written to GCF_002930645.1_ASM293064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:09,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:09,543] [INFO] DFAST_QC result json was written to GCF_002930645.1_ASM293064v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:09,543] [INFO] DFAST_QC completed!
[2024-01-24 15:04:09,543] [INFO] Total running time: 0h1m32s