[2023-06-17 07:53:25,133] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:53:25,151] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:53:25,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg8efae87f-72a5-4082-867b-8f9166f3e3a2/dqc_reference
[2023-06-17 07:53:26,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:53:26,419] [INFO] Task started: Prodigal
[2023-06-17 07:53:26,420] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d562640-09ea-4e88-b35e-8fe810f1005c/GCA_013607665.1_ASM1360766v1_genomic.fna.gz | prodigal -d GCA_013607665.1_ASM1360766v1_genomic.fna/cds.fna -a GCA_013607665.1_ASM1360766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:53:29,604] [INFO] Task succeeded: Prodigal
[2023-06-17 07:53:29,605] [INFO] Task started: HMMsearch
[2023-06-17 07:53:29,605] [INFO] Running command: hmmsearch --tblout GCA_013607665.1_ASM1360766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8efae87f-72a5-4082-867b-8f9166f3e3a2/dqc_reference/reference_markers.hmm GCA_013607665.1_ASM1360766v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:53:29,825] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:53:29,827] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7d562640-09ea-4e88-b35e-8fe810f1005c/GCA_013607665.1_ASM1360766v1_genomic.fna.gz]
[2023-06-17 07:53:29,856] [INFO] Query marker FASTA was written to GCA_013607665.1_ASM1360766v1_genomic.fna/markers.fasta
[2023-06-17 07:53:29,857] [INFO] Task started: Blastn
[2023-06-17 07:53:29,857] [INFO] Running command: blastn -query GCA_013607665.1_ASM1360766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8efae87f-72a5-4082-867b-8f9166f3e3a2/dqc_reference/reference_markers.fasta -out GCA_013607665.1_ASM1360766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:53:30,442] [INFO] Task succeeded: Blastn
[2023-06-17 07:53:30,447] [INFO] Selected 13 target genomes.
[2023-06-17 07:53:30,448] [INFO] Target genome list was writen to GCA_013607665.1_ASM1360766v1_genomic.fna/target_genomes.txt
[2023-06-17 07:53:30,451] [INFO] Task started: fastANI
[2023-06-17 07:53:30,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d562640-09ea-4e88-b35e-8fe810f1005c/GCA_013607665.1_ASM1360766v1_genomic.fna.gz --refList GCA_013607665.1_ASM1360766v1_genomic.fna/target_genomes.txt --output GCA_013607665.1_ASM1360766v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:53:35,037] [INFO] Task succeeded: fastANI
[2023-06-17 07:53:35,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8efae87f-72a5-4082-867b-8f9166f3e3a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:53:35,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8efae87f-72a5-4082-867b-8f9166f3e3a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:53:35,050] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 07:53:35,050] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 07:53:35,050] [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
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	82.321	347	443	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	81.4662	337	443	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	79.2947	216	443	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	78.71	200	443	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	78.696	211	443	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	78.1446	100	443	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	77.8695	101	443	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	77.5156	119	443	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.4497	118	443	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 07:53:35,052] [INFO] DFAST Taxonomy check result was written to GCA_013607665.1_ASM1360766v1_genomic.fna/tc_result.tsv
[2023-06-17 07:53:35,053] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:53:35,054] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:53:35,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8efae87f-72a5-4082-867b-8f9166f3e3a2/dqc_reference/checkm_data
[2023-06-17 07:53:35,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:53:35,079] [INFO] Task started: CheckM
[2023-06-17 07:53:35,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013607665.1_ASM1360766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013607665.1_ASM1360766v1_genomic.fna/checkm_input GCA_013607665.1_ASM1360766v1_genomic.fna/checkm_result
[2023-06-17 07:53:52,656] [INFO] Task succeeded: CheckM
[2023-06-17 07:53:52,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 07:53:52,682] [INFO] ===== Completeness check finished =====
[2023-06-17 07:53:52,683] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:53:52,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013607665.1_ASM1360766v1_genomic.fna/markers.fasta)
[2023-06-17 07:53:52,683] [INFO] Task started: Blastn
[2023-06-17 07:53:52,683] [INFO] Running command: blastn -query GCA_013607665.1_ASM1360766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8efae87f-72a5-4082-867b-8f9166f3e3a2/dqc_reference/reference_markers_gtdb.fasta -out GCA_013607665.1_ASM1360766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:53:53,475] [INFO] Task succeeded: Blastn
[2023-06-17 07:53:53,480] [INFO] Selected 12 target genomes.
[2023-06-17 07:53:53,481] [INFO] Target genome list was writen to GCA_013607665.1_ASM1360766v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:53:53,486] [INFO] Task started: fastANI
[2023-06-17 07:53:53,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d562640-09ea-4e88-b35e-8fe810f1005c/GCA_013607665.1_ASM1360766v1_genomic.fna.gz --refList GCA_013607665.1_ASM1360766v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013607665.1_ASM1360766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:53:58,311] [INFO] Task succeeded: fastANI
[2023-06-17 07:53:58,322] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:53:58,323] [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_013607665.1	s__Sulfurimonas sp013607665	100.0	432	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009192995.1	s__Sulfurimonas indica	82.321	347	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905135.1	s__Sulfurimonas paralvinellae	81.4795	336	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147355.1	s__Sulfurimonas autotrophica	79.2947	216	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009068765.1	s__Sulfurimonas sp009068765	78.71	200	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905095.1	s__Sulfurimonas sp014905095	78.5423	156	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015662405.1	s__Sulfurimonas autotrophica_A	78.3953	139	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488615.1	s__Sulfurimonas sp015488615	78.1993	123	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.68	99.68	0.82	0.82	2	-
GCF_017357825.1	s__Sulfurimonas sp017357825	77.9506	118	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487265.1	s__Sulfurimonas sp015487265	77.9184	143	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381585.1	s__Sulfurimonas ponti	77.5558	91	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	99.38	0.90	0.90	2	-
GCA_903885085.1	s__CAITKP01 sp903885085	77.28	79	443	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__CAITKP01	95.0	99.50	98.51	0.91	0.85	21	-
--------------------------------------------------------------------------------
[2023-06-17 07:53:58,326] [INFO] GTDB search result was written to GCA_013607665.1_ASM1360766v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:53:58,326] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:53:58,330] [INFO] DFAST_QC result json was written to GCA_013607665.1_ASM1360766v1_genomic.fna/dqc_result.json
[2023-06-17 07:53:58,330] [INFO] DFAST_QC completed!
[2023-06-17 07:53:58,330] [INFO] Total running time: 0h0m33s