[2024-01-25 19:58:50,751] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:50,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:50,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a689630-5042-4082-9876-f8ae801bb89a/dqc_reference
[2024-01-25 19:58:51,911] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:51,912] [INFO] Task started: Prodigal
[2024-01-25 19:58:51,912] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3dfb5d2-3049-4c31-918f-a669a0cfa4af/GCF_003052265.1_ASM305226v1_genomic.fna.gz | prodigal -d GCF_003052265.1_ASM305226v1_genomic.fna/cds.fna -a GCF_003052265.1_ASM305226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:02,899] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:02,900] [INFO] Task started: HMMsearch
[2024-01-25 19:59:02,900] [INFO] Running command: hmmsearch --tblout GCF_003052265.1_ASM305226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a689630-5042-4082-9876-f8ae801bb89a/dqc_reference/reference_markers.hmm GCF_003052265.1_ASM305226v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:03,152] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:03,154] [INFO] Found 6/6 markers.
[2024-01-25 19:59:03,185] [INFO] Query marker FASTA was written to GCF_003052265.1_ASM305226v1_genomic.fna/markers.fasta
[2024-01-25 19:59:03,185] [INFO] Task started: Blastn
[2024-01-25 19:59:03,185] [INFO] Running command: blastn -query GCF_003052265.1_ASM305226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a689630-5042-4082-9876-f8ae801bb89a/dqc_reference/reference_markers.fasta -out GCF_003052265.1_ASM305226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:03,880] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:03,882] [INFO] Selected 23 target genomes.
[2024-01-25 19:59:03,882] [INFO] Target genome list was writen to GCF_003052265.1_ASM305226v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:03,930] [INFO] Task started: fastANI
[2024-01-25 19:59:03,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3dfb5d2-3049-4c31-918f-a669a0cfa4af/GCF_003052265.1_ASM305226v1_genomic.fna.gz --refList GCF_003052265.1_ASM305226v1_genomic.fna/target_genomes.txt --output GCF_003052265.1_ASM305226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:20,118] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:20,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a689630-5042-4082-9876-f8ae801bb89a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:20,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a689630-5042-4082-9876-f8ae801bb89a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:20,132] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:20,132] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:20,132] [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
Stenotrophobium rhamnosiphilum	strain=GT1R17	GCA_003052265.1	2029166	2029166	type	True	100.0	1309	1309	95	conclusive
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	77.2553	149	1309	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	77.0154	182	1309	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	76.9322	175	1309	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	76.8539	172	1309	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	76.7855	141	1309	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	76.7785	174	1309	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	76.7732	179	1309	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	76.7476	159	1309	95	below_threshold
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	76.5058	105	1309	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	76.4223	93	1309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:20,133] [INFO] DFAST Taxonomy check result was written to GCF_003052265.1_ASM305226v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:20,134] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:20,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:20,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a689630-5042-4082-9876-f8ae801bb89a/dqc_reference/checkm_data
[2024-01-25 19:59:20,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:20,177] [INFO] Task started: CheckM
[2024-01-25 19:59:20,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003052265.1_ASM305226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003052265.1_ASM305226v1_genomic.fna/checkm_input GCF_003052265.1_ASM305226v1_genomic.fna/checkm_result
[2024-01-25 19:59:54,305] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:54,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:54,324] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:54,324] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:54,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003052265.1_ASM305226v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:54,324] [INFO] Task started: Blastn
[2024-01-25 19:59:54,324] [INFO] Running command: blastn -query GCF_003052265.1_ASM305226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a689630-5042-4082-9876-f8ae801bb89a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003052265.1_ASM305226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:55,503] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:55,505] [INFO] Selected 20 target genomes.
[2024-01-25 19:59:55,505] [INFO] Target genome list was writen to GCF_003052265.1_ASM305226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:55,526] [INFO] Task started: fastANI
[2024-01-25 19:59:55,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3dfb5d2-3049-4c31-918f-a669a0cfa4af/GCF_003052265.1_ASM305226v1_genomic.fna.gz --refList GCF_003052265.1_ASM305226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003052265.1_ASM305226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:09,721] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:09,732] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:09,732] [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_003052265.1	s__Stenotrophobium rhamnosiphilum	100.0	1309	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008012115.1	s__Stenotrophobium sp008012115	77.9357	363	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129825.1	s__Hydrocarboniphaga daqingensis	77.2553	149	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	77.0144	182	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047655.1	s__CAU-1509 sp005047655	76.9983	130	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__CAU-1509	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	76.9323	175	1309	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_003428335.1	s__Solimonas_A sp003428335	76.8882	207	1309	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_000382285.1	s__Solimonas variicoloris	76.867	171	1309	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	76.8399	164	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	76.7914	173	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	76.7853	178	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_003730135.1	s__Stagnimonas aquatica	76.7501	152	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	76.7476	159	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970615.1	s__Nevskia sp903970615	76.5852	117	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822975.1	s__Nevskia sp903822975	76.5816	142	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	100.00	100.00	0.99	0.99	2	-
GCA_004297005.1	s__Stagnimonas sp004297005	76.578	126	1309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:09,733] [INFO] GTDB search result was written to GCF_003052265.1_ASM305226v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:09,734] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:09,737] [INFO] DFAST_QC result json was written to GCF_003052265.1_ASM305226v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:09,737] [INFO] DFAST_QC completed!
[2024-01-25 20:00:09,737] [INFO] Total running time: 0h1m19s