[2024-01-24 15:19:03,912] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:03,914] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:03,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg35512b7e-0caa-409f-9557-f6d1559b14a0/dqc_reference
[2024-01-24 15:19:05,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,144] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,144] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2cdff34-0816-457d-966b-e23e305b6ec3/GCF_004216565.1_ASM421656v1_genomic.fna.gz | prodigal -d GCF_004216565.1_ASM421656v1_genomic.fna/cds.fna -a GCF_004216565.1_ASM421656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:20,460] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:20,460] [INFO] Task started: HMMsearch
[2024-01-24 15:19:20,461] [INFO] Running command: hmmsearch --tblout GCF_004216565.1_ASM421656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35512b7e-0caa-409f-9557-f6d1559b14a0/dqc_reference/reference_markers.hmm GCF_004216565.1_ASM421656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:20,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:20,754] [INFO] Found 6/6 markers.
[2024-01-24 15:19:20,798] [INFO] Query marker FASTA was written to GCF_004216565.1_ASM421656v1_genomic.fna/markers.fasta
[2024-01-24 15:19:20,798] [INFO] Task started: Blastn
[2024-01-24 15:19:20,798] [INFO] Running command: blastn -query GCF_004216565.1_ASM421656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35512b7e-0caa-409f-9557-f6d1559b14a0/dqc_reference/reference_markers.fasta -out GCF_004216565.1_ASM421656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:21,865] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:21,869] [INFO] Selected 16 target genomes.
[2024-01-24 15:19:21,869] [INFO] Target genome list was writen to GCF_004216565.1_ASM421656v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:21,877] [INFO] Task started: fastANI
[2024-01-24 15:19:21,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2cdff34-0816-457d-966b-e23e305b6ec3/GCF_004216565.1_ASM421656v1_genomic.fna.gz --refList GCF_004216565.1_ASM421656v1_genomic.fna/target_genomes.txt --output GCF_004216565.1_ASM421656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:37,533] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:37,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35512b7e-0caa-409f-9557-f6d1559b14a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:37,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35512b7e-0caa-409f-9557-f6d1559b14a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:37,551] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:37,551] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:37,551] [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
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	82.3314	840	1544	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	82.284	822	1544	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	82.223	813	1544	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	82.1174	818	1544	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	81.8253	838	1544	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	81.8248	860	1544	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.7785	642	1544	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.6454	638	1544	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.6307	635	1544	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.5758	642	1544	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.3918	604	1544	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.9564	745	1544	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.8315	632	1544	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.7434	646	1544	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.6371	517	1544	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.5677	667	1544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:37,553] [INFO] DFAST Taxonomy check result was written to GCF_004216565.1_ASM421656v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:37,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:37,554] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:37,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35512b7e-0caa-409f-9557-f6d1559b14a0/dqc_reference/checkm_data
[2024-01-24 15:19:37,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:37,599] [INFO] Task started: CheckM
[2024-01-24 15:19:37,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004216565.1_ASM421656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004216565.1_ASM421656v1_genomic.fna/checkm_input GCF_004216565.1_ASM421656v1_genomic.fna/checkm_result
[2024-01-24 15:21:13,110] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:13,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:13,130] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:13,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:13,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004216565.1_ASM421656v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:13,132] [INFO] Task started: Blastn
[2024-01-24 15:21:13,132] [INFO] Running command: blastn -query GCF_004216565.1_ASM421656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35512b7e-0caa-409f-9557-f6d1559b14a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004216565.1_ASM421656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:15,408] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:15,411] [INFO] Selected 17 target genomes.
[2024-01-24 15:21:15,412] [INFO] Target genome list was writen to GCF_004216565.1_ASM421656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:15,426] [INFO] Task started: fastANI
[2024-01-24 15:21:15,426] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2cdff34-0816-457d-966b-e23e305b6ec3/GCF_004216565.1_ASM421656v1_genomic.fna.gz --refList GCF_004216565.1_ASM421656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004216565.1_ASM421656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:36,398] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:36,425] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:36,425] [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_004216565.1	s__Leptothrix mobilis	100.0	1542	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000019785.1	s__Leptothrix cholodnii	83.6874	1023	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201595.1	s__Sphaerotilus hippei	82.3182	840	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156335.1	s__Sphaerotilus natans	82.2767	823	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013294065.1	s__Sphaerotilus sp013294065	82.2477	850	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329925.1	s__Sphaerotilus sulfidivorans	82.1626	830	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013410775.1	s__Sphaerotilus montanus	81.8049	861	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013299055.1	s__Sphaerotilus sp013299055	80.9188	623	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	80.8914	803	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	80.7352	689	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	80.6097	636	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCF_001984095.1	s__KK5 sp001984095	80.0875	729	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__KK5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266755.1	s__Aquabacterium_A terrae	80.006	764	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938815.1	s__Rubrivivax sp903938815	79.9553	628	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.66	99.41	0.96	0.94	10	-
GCF_009760915.1	s__Azohydromonas aeria	79.9325	747	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322345.1	s__Aquabacterium sp004322345	79.9089	545	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.53	97.53	0.87	0.87	2	-
GCA_019237615.1	s__Pelomonas sp019237615	79.7013	590	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:36,427] [INFO] GTDB search result was written to GCF_004216565.1_ASM421656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:36,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:36,431] [INFO] DFAST_QC result json was written to GCF_004216565.1_ASM421656v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:36,431] [INFO] DFAST_QC completed!
[2024-01-24 15:21:36,431] [INFO] Total running time: 0h2m33s