[2023-06-04 17:30:43,484] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:30:43,488] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:30:43,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg72def321-f22f-4ce7-835d-076e101c4a31/dqc_reference
[2023-06-04 17:30:45,168] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:30:45,170] [INFO] Task started: Prodigal
[2023-06-04 17:30:45,170] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a7c2ccd-3581-4a46-9e64-ebdf03853e06/GCA_004297005.1_ASM429700v1_genomic.fna.gz | prodigal -d GCA_004297005.1_ASM429700v1_genomic.fna/cds.fna -a GCA_004297005.1_ASM429700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:30:55,011] [INFO] Task succeeded: Prodigal
[2023-06-04 17:30:55,011] [INFO] Task started: HMMsearch
[2023-06-04 17:30:55,011] [INFO] Running command: hmmsearch --tblout GCA_004297005.1_ASM429700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72def321-f22f-4ce7-835d-076e101c4a31/dqc_reference/reference_markers.hmm GCA_004297005.1_ASM429700v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:30:55,279] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:30:55,280] [INFO] Found 6/6 markers.
[2023-06-04 17:30:55,312] [INFO] Query marker FASTA was written to GCA_004297005.1_ASM429700v1_genomic.fna/markers.fasta
[2023-06-04 17:30:55,313] [INFO] Task started: Blastn
[2023-06-04 17:30:55,313] [INFO] Running command: blastn -query GCA_004297005.1_ASM429700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72def321-f22f-4ce7-835d-076e101c4a31/dqc_reference/reference_markers.fasta -out GCA_004297005.1_ASM429700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:30:56,219] [INFO] Task succeeded: Blastn
[2023-06-04 17:30:56,224] [INFO] Selected 22 target genomes.
[2023-06-04 17:30:56,224] [INFO] Target genome list was writen to GCA_004297005.1_ASM429700v1_genomic.fna/target_genomes.txt
[2023-06-04 17:30:57,048] [INFO] Task started: fastANI
[2023-06-04 17:30:57,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a7c2ccd-3581-4a46-9e64-ebdf03853e06/GCA_004297005.1_ASM429700v1_genomic.fna.gz --refList GCA_004297005.1_ASM429700v1_genomic.fna/target_genomes.txt --output GCA_004297005.1_ASM429700v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:31:14,953] [INFO] Task succeeded: fastANI
[2023-06-04 17:31:14,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72def321-f22f-4ce7-835d-076e101c4a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:31:14,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72def321-f22f-4ce7-835d-076e101c4a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:31:14,970] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:31:14,970] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:31:14,971] [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	79.4842	530	1159	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	78.9012	485	1159	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	78.8041	482	1159	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	78.7885	479	1159	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	78.7427	481	1159	95	below_threshold
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	78.1691	359	1159	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	78.1631	379	1159	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	78.0889	363	1159	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	78.0491	383	1159	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	77.9717	384	1159	95	below_threshold
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	77.9017	321	1159	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	77.7818	300	1159	95	below_threshold
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	77.5318	241	1159	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	77.289	236	1159	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.9228	190	1159	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	76.9043	220	1159	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.8272	256	1159	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	76.7334	238	1159	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.7079	239	1159	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.3496	236	1159	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	76.2905	235	1159	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	76.0909	124	1159	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:31:14,973] [INFO] DFAST Taxonomy check result was written to GCA_004297005.1_ASM429700v1_genomic.fna/tc_result.tsv
[2023-06-04 17:31:14,974] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:31:14,974] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:31:14,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72def321-f22f-4ce7-835d-076e101c4a31/dqc_reference/checkm_data
[2023-06-04 17:31:14,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:31:15,012] [INFO] Task started: CheckM
[2023-06-04 17:31:15,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004297005.1_ASM429700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004297005.1_ASM429700v1_genomic.fna/checkm_input GCA_004297005.1_ASM429700v1_genomic.fna/checkm_result
[2023-06-04 17:31:47,589] [INFO] Task succeeded: CheckM
[2023-06-04 17:31:47,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:31:47,612] [INFO] ===== Completeness check finished =====
[2023-06-04 17:31:47,612] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:31:47,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004297005.1_ASM429700v1_genomic.fna/markers.fasta)
[2023-06-04 17:31:47,613] [INFO] Task started: Blastn
[2023-06-04 17:31:47,613] [INFO] Running command: blastn -query GCA_004297005.1_ASM429700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72def321-f22f-4ce7-835d-076e101c4a31/dqc_reference/reference_markers_gtdb.fasta -out GCA_004297005.1_ASM429700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:31:49,379] [INFO] Task succeeded: Blastn
[2023-06-04 17:31:49,389] [INFO] Selected 13 target genomes.
[2023-06-04 17:31:49,389] [INFO] Target genome list was writen to GCA_004297005.1_ASM429700v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:31:49,762] [INFO] Task started: fastANI
[2023-06-04 17:31:49,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a7c2ccd-3581-4a46-9e64-ebdf03853e06/GCA_004297005.1_ASM429700v1_genomic.fna.gz --refList GCA_004297005.1_ASM429700v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004297005.1_ASM429700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:32:02,028] [INFO] Task succeeded: fastANI
[2023-06-04 17:32:02,043] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:32:02,044] [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
GCA_004297005.1	s__Stagnimonas sp004297005	100.0	1158	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	conclusive
GCF_003730135.1	s__Stagnimonas aquatica	89.9465	983	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	79.4769	567	1159	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	79.442	534	1159	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	79.2369	469	1159	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	78.8724	488	1159	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	78.8197	468	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711955.1	s__Nevskia soli	78.8051	482	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	78.7449	480	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	78.6026	381	1159	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	78.1637	380	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016918765.1	s__Polycyclovorans sp016918765	77.7706	301	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822975.1	s__Nevskia sp903822975	77.6344	291	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-04 17:32:02,046] [INFO] GTDB search result was written to GCA_004297005.1_ASM429700v1_genomic.fna/result_gtdb.tsv
[2023-06-04 17:32:02,046] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:32:02,051] [INFO] DFAST_QC result json was written to GCA_004297005.1_ASM429700v1_genomic.fna/dqc_result.json
[2023-06-04 17:32:02,051] [INFO] DFAST_QC completed!
[2023-06-04 17:32:02,051] [INFO] Total running time: 0h1m19s