[2024-01-24 12:45:09,801] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:09,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:09,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc743dc2-75f1-4c76-a2d8-1b0a4d45010f/dqc_reference
[2024-01-24 12:45:13,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,082] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg8922822f-8983-4277-bef8-ef9e810109bf/GCF_004342485.1_ASM434248v1_genomic.fna.gz | prodigal -d GCF_004342485.1_ASM434248v1_genomic.fna/cds.fna -a GCF_004342485.1_ASM434248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:29,924] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:29,925] [INFO] Task started: HMMsearch
[2024-01-24 12:45:29,925] [INFO] Running command: hmmsearch --tblout GCF_004342485.1_ASM434248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc743dc2-75f1-4c76-a2d8-1b0a4d45010f/dqc_reference/reference_markers.hmm GCF_004342485.1_ASM434248v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:30,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:30,230] [INFO] Found 6/6 markers.
[2024-01-24 12:45:30,279] [INFO] Query marker FASTA was written to GCF_004342485.1_ASM434248v1_genomic.fna/markers.fasta
[2024-01-24 12:45:30,279] [INFO] Task started: Blastn
[2024-01-24 12:45:30,280] [INFO] Running command: blastn -query GCF_004342485.1_ASM434248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc743dc2-75f1-4c76-a2d8-1b0a4d45010f/dqc_reference/reference_markers.fasta -out GCF_004342485.1_ASM434248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:31,224] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:31,228] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:31,229] [INFO] Target genome list was writen to GCF_004342485.1_ASM434248v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:31,244] [INFO] Task started: fastANI
[2024-01-24 12:45:31,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg8922822f-8983-4277-bef8-ef9e810109bf/GCF_004342485.1_ASM434248v1_genomic.fna.gz --refList GCF_004342485.1_ASM434248v1_genomic.fna/target_genomes.txt --output GCF_004342485.1_ASM434248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:55,897] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:55,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc743dc2-75f1-4c76-a2d8-1b0a4d45010f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:55,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc743dc2-75f1-4c76-a2d8-1b0a4d45010f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:55,919] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:55,920] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:55,920] [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
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	100.0	1861	1863	95	conclusive
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	85.1394	1215	1863	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	80.9696	879	1863	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.4808	713	1863	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.4774	702	1863	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.3739	738	1863	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	80.2402	849	1863	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.0428	673	1863	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.0424	709	1863	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	79.974	797	1863	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	79.9697	758	1863	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	79.7677	685	1863	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.5459	791	1863	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.4271	710	1863	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	79.4043	712	1863	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	79.3255	529	1863	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.1723	617	1863	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	79.0506	606	1863	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.0494	636	1863	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.0249	574	1863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:55,922] [INFO] DFAST Taxonomy check result was written to GCF_004342485.1_ASM434248v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:55,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:55,923] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:55,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc743dc2-75f1-4c76-a2d8-1b0a4d45010f/dqc_reference/checkm_data
[2024-01-24 12:45:55,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:55,980] [INFO] Task started: CheckM
[2024-01-24 12:45:55,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342485.1_ASM434248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342485.1_ASM434248v1_genomic.fna/checkm_input GCF_004342485.1_ASM434248v1_genomic.fna/checkm_result
[2024-01-24 12:46:55,822] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:55,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:55,851] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:55,851] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:55,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342485.1_ASM434248v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:55,852] [INFO] Task started: Blastn
[2024-01-24 12:46:55,852] [INFO] Running command: blastn -query GCF_004342485.1_ASM434248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc743dc2-75f1-4c76-a2d8-1b0a4d45010f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342485.1_ASM434248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:57,557] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:57,561] [INFO] Selected 14 target genomes.
[2024-01-24 12:46:57,562] [INFO] Target genome list was writen to GCF_004342485.1_ASM434248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:57,580] [INFO] Task started: fastANI
[2024-01-24 12:46:57,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg8922822f-8983-4277-bef8-ef9e810109bf/GCF_004342485.1_ASM434248v1_genomic.fna.gz --refList GCF_004342485.1_ASM434248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342485.1_ASM434248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:17,771] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:17,791] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:17,791] [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_004342485.1	s__Pelomonas saccharophila	100.0	1861	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009996515.1	s__Pelomonas sp009996515	87.5773	1115	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237615.1	s__Pelomonas sp019237615	87.2152	1122	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550215.1	s__Pelomonas sp003550215	86.7525	1265	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426885.1	s__Pelomonas sp001426885	86.6835	1233	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425055.1	s__Pelomonas sp001425055	86.5469	1272	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963075.1	s__Pelomonas sp003963075	86.5194	1037	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	96.90	96.90	0.86	0.86	2	-
GCA_016195825.1	s__Pelomonas sp016195825	86.2618	1185	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425705.1	s__Pelomonas sp001425705	86.2175	1284	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205845.1	s__Pelomonas puraquae	85.1498	1214	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963005.1	s__Pelomonas sp003963005	84.9172	1134	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984095.1	s__KK5 sp001984095	81.9483	951	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__KK5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425825.1	s__Rhizobacter sp001425825	79.647	820	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	99.93	99.87	0.98	0.98	3	-
GCA_018241265.1	s__JAFEEF01 sp018241265	79.1185	672	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFEEF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:17,793] [INFO] GTDB search result was written to GCF_004342485.1_ASM434248v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:17,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:17,798] [INFO] DFAST_QC result json was written to GCF_004342485.1_ASM434248v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:17,798] [INFO] DFAST_QC completed!
[2024-01-24 12:47:17,798] [INFO] Total running time: 0h2m8s