[2024-01-24 13:58:41,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:41,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:41,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg733b3d44-fd0b-4b58-9eed-d228971879be/dqc_reference
[2024-01-24 13:58:43,283] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:43,284] [INFO] Task started: Prodigal
[2024-01-24 13:58:43,284] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6126d8a-7419-4add-be23-55f4540bbab5/GCF_003730135.1_ASM373013v1_genomic.fna.gz | prodigal -d GCF_003730135.1_ASM373013v1_genomic.fna/cds.fna -a GCF_003730135.1_ASM373013v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:54,762] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:54,763] [INFO] Task started: HMMsearch
[2024-01-24 13:58:54,763] [INFO] Running command: hmmsearch --tblout GCF_003730135.1_ASM373013v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg733b3d44-fd0b-4b58-9eed-d228971879be/dqc_reference/reference_markers.hmm GCF_003730135.1_ASM373013v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:55,057] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:55,059] [INFO] Found 6/6 markers.
[2024-01-24 13:58:55,094] [INFO] Query marker FASTA was written to GCF_003730135.1_ASM373013v1_genomic.fna/markers.fasta
[2024-01-24 13:58:55,095] [INFO] Task started: Blastn
[2024-01-24 13:58:55,095] [INFO] Running command: blastn -query GCF_003730135.1_ASM373013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg733b3d44-fd0b-4b58-9eed-d228971879be/dqc_reference/reference_markers.fasta -out GCF_003730135.1_ASM373013v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:56,054] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:56,059] [INFO] Selected 24 target genomes.
[2024-01-24 13:58:56,060] [INFO] Target genome list was writen to GCF_003730135.1_ASM373013v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:56,074] [INFO] Task started: fastANI
[2024-01-24 13:58:56,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6126d8a-7419-4add-be23-55f4540bbab5/GCF_003730135.1_ASM373013v1_genomic.fna.gz --refList GCF_003730135.1_ASM373013v1_genomic.fna/target_genomes.txt --output GCF_003730135.1_ASM373013v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:13,892] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:13,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg733b3d44-fd0b-4b58-9eed-d228971879be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:13,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg733b3d44-fd0b-4b58-9eed-d228971879be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:13,913] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:13,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:13,914] [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	79.6602	589	1257	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	78.952	533	1257	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	78.9123	538	1257	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	78.8443	489	1257	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	78.798	530	1257	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	78.7546	547	1257	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	78.3067	425	1257	95	below_threshold
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	78.2797	365	1257	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	78.2331	329	1257	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	78.2072	397	1257	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	78.1893	419	1257	95	below_threshold
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	78.0983	400	1257	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	77.966	417	1257	95	below_threshold
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	77.7582	280	1257	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.1482	206	1257	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	77.0401	247	1257	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	77.0048	300	1257	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	76.8627	173	1257	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.769	269	1257	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.6246	292	1257	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.5946	270	1257	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	76.5201	164	1257	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.3495	122	1257	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	76.1306	246	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:13,916] [INFO] DFAST Taxonomy check result was written to GCF_003730135.1_ASM373013v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:13,916] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:13,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:13,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg733b3d44-fd0b-4b58-9eed-d228971879be/dqc_reference/checkm_data
[2024-01-24 13:59:13,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:13,956] [INFO] Task started: CheckM
[2024-01-24 13:59:13,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003730135.1_ASM373013v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003730135.1_ASM373013v1_genomic.fna/checkm_input GCF_003730135.1_ASM373013v1_genomic.fna/checkm_result
[2024-01-24 13:59:48,340] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:48,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:48,364] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:48,364] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:48,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003730135.1_ASM373013v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:48,365] [INFO] Task started: Blastn
[2024-01-24 13:59:48,365] [INFO] Running command: blastn -query GCF_003730135.1_ASM373013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg733b3d44-fd0b-4b58-9eed-d228971879be/dqc_reference/reference_markers_gtdb.fasta -out GCF_003730135.1_ASM373013v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:50,098] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:50,105] [INFO] Selected 14 target genomes.
[2024-01-24 13:59:50,105] [INFO] Target genome list was writen to GCF_003730135.1_ASM373013v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:50,127] [INFO] Task started: fastANI
[2024-01-24 13:59:50,128] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6126d8a-7419-4add-be23-55f4540bbab5/GCF_003730135.1_ASM373013v1_genomic.fna.gz --refList GCF_003730135.1_ASM373013v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003730135.1_ASM373013v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:02,410] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:02,425] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:02,426] [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_003730135.1	s__Stagnimonas aquatica	100.0	1255	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004297005.1	s__Stagnimonas sp004297005	90.0134	965	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
GCF_003428335.1	s__Solimonas_A sp003428335	79.8315	579	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	79.6445	591	1257	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	79.4064	481	1257	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	78.7965	552	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000711955.1	s__Nevskia soli	78.7747	533	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	78.6802	430	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	78.5557	496	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823855.1	s__Nevskia sp013823855	78.5228	417	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	78.3127	425	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	78.1284	426	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822975.1	s__Nevskia sp903822975	77.3944	339	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	100.00	100.00	0.99	0.99	2	-
GCA_903970615.1	s__Nevskia sp903970615	77.0465	198	1257	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 14:00:02,427] [INFO] GTDB search result was written to GCF_003730135.1_ASM373013v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:02,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:02,433] [INFO] DFAST_QC result json was written to GCF_003730135.1_ASM373013v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:02,433] [INFO] DFAST_QC completed!
[2024-01-24 14:00:02,433] [INFO] Total running time: 0h1m21s