[2024-01-24 15:32:03,718] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:03,721] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:03,721] [INFO] DQC Reference Directory: /var/lib/cwl/stg17e553d7-2169-4cbe-a0c7-fb1ba7ddb5b3/dqc_reference
[2024-01-24 15:32:04,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:04,921] [INFO] Task started: Prodigal
[2024-01-24 15:32:04,921] [INFO] Running command: gunzip -c /var/lib/cwl/stga3a7eea7-3ae8-47ae-ac4e-84ef5ec790ae/GCF_001595985.1_ASM159598v1_genomic.fna.gz | prodigal -d GCF_001595985.1_ASM159598v1_genomic.fna/cds.fna -a GCF_001595985.1_ASM159598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:10,690] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:10,691] [INFO] Task started: HMMsearch
[2024-01-24 15:32:10,691] [INFO] Running command: hmmsearch --tblout GCF_001595985.1_ASM159598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17e553d7-2169-4cbe-a0c7-fb1ba7ddb5b3/dqc_reference/reference_markers.hmm GCF_001595985.1_ASM159598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:10,936] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:10,937] [INFO] Found 6/6 markers.
[2024-01-24 15:32:10,963] [INFO] Query marker FASTA was written to GCF_001595985.1_ASM159598v1_genomic.fna/markers.fasta
[2024-01-24 15:32:10,964] [INFO] Task started: Blastn
[2024-01-24 15:32:10,964] [INFO] Running command: blastn -query GCF_001595985.1_ASM159598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17e553d7-2169-4cbe-a0c7-fb1ba7ddb5b3/dqc_reference/reference_markers.fasta -out GCF_001595985.1_ASM159598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:11,580] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:11,584] [INFO] Selected 10 target genomes.
[2024-01-24 15:32:11,584] [INFO] Target genome list was writen to GCF_001595985.1_ASM159598v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:11,587] [INFO] Task started: fastANI
[2024-01-24 15:32:11,588] [INFO] Running command: fastANI --query /var/lib/cwl/stga3a7eea7-3ae8-47ae-ac4e-84ef5ec790ae/GCF_001595985.1_ASM159598v1_genomic.fna.gz --refList GCF_001595985.1_ASM159598v1_genomic.fna/target_genomes.txt --output GCF_001595985.1_ASM159598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:15,927] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:15,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17e553d7-2169-4cbe-a0c7-fb1ba7ddb5b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:15,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17e553d7-2169-4cbe-a0c7-fb1ba7ddb5b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:15,945] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:32:15,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:15,946] [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
Polynucleobacter sinensis	strain=MWH-HuW1	GCA_001595985.1	1743157	1743157	type	True	100.0	764	765	95	conclusive
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	81.23	349	765	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	81.139	363	765	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	80.8938	369	765	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	80.8181	342	765	95	below_threshold
Polynucleobacter duraquae	strain=MWH-MoK4	GCA_000973625.1	1835254	1835254	type	True	80.7714	358	765	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	80.7486	351	765	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	80.5424	329	765	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	80.366	294	765	95	below_threshold
Polynucleobacter antarcticus	strain=LimPoW16	GCA_013307245.1	1743162	1743162	type	True	79.3433	304	765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:15,948] [INFO] DFAST Taxonomy check result was written to GCF_001595985.1_ASM159598v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:15,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:15,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:15,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17e553d7-2169-4cbe-a0c7-fb1ba7ddb5b3/dqc_reference/checkm_data
[2024-01-24 15:32:15,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:15,980] [INFO] Task started: CheckM
[2024-01-24 15:32:15,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001595985.1_ASM159598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001595985.1_ASM159598v1_genomic.fna/checkm_input GCF_001595985.1_ASM159598v1_genomic.fna/checkm_result
[2024-01-24 15:32:39,607] [INFO] Task succeeded: CheckM
[2024-01-24 15:32:39,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:32:39,628] [INFO] ===== Completeness check finished =====
[2024-01-24 15:32:39,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:32:39,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001595985.1_ASM159598v1_genomic.fna/markers.fasta)
[2024-01-24 15:32:39,630] [INFO] Task started: Blastn
[2024-01-24 15:32:39,630] [INFO] Running command: blastn -query GCF_001595985.1_ASM159598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17e553d7-2169-4cbe-a0c7-fb1ba7ddb5b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001595985.1_ASM159598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:40,463] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:40,469] [INFO] Selected 19 target genomes.
[2024-01-24 15:32:40,469] [INFO] Target genome list was writen to GCF_001595985.1_ASM159598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:32:40,500] [INFO] Task started: fastANI
[2024-01-24 15:32:40,500] [INFO] Running command: fastANI --query /var/lib/cwl/stga3a7eea7-3ae8-47ae-ac4e-84ef5ec790ae/GCF_001595985.1_ASM159598v1_genomic.fna.gz --refList GCF_001595985.1_ASM159598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001595985.1_ASM159598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:32:49,173] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:49,192] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:32:49,192] [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_001595985.1	s__Polynucleobacter sinensis	100.0	764	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018882405.1	s__Polynucleobacter sp018882405	82.0008	391	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882325.1	s__Polynucleobacter sp018882325	81.9587	403	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882335.1	s__Polynucleobacter sp018882335	81.8792	374	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882055.1	s__Polynucleobacter sp018882055	81.7906	368	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000342265.1	s__Polynucleobacter sp000342265	81.7802	396	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881905.1	s__Polynucleobacter sp018881905	81.777	395	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882295.1	s__Polynucleobacter sp018882295	81.7536	402	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687575.1	s__Polynucleobacter asymbioticus_C	81.7001	365	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688235.1	s__Polynucleobacter sp018688235	81.5688	393	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688375.1	s__Polynucleobacter sp018688375	81.5442	386	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900095165.1	s__Polynucleobacter necessarius_J	81.3836	357	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830325.1	s__Polynucleobacter sp001830325	81.3176	381	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018688335.1	s__Polynucleobacter sp018688335	81.3153	364	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	95.20	95.20	0.89	0.89	2	-
GCF_018687755.1	s__Polynucleobacter sp018687755	81.004	358	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688355.1	s__Polynucleobacter sp018688355	80.8132	360	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881505.1	s__Polynucleobacter sp018881505	80.6845	386	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881795.1	s__Polynucleobacter sp018881795	80.5195	319	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882095.1	s__Polynucleobacter sp018882095	80.1805	336	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:32:49,194] [INFO] GTDB search result was written to GCF_001595985.1_ASM159598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:32:49,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:32:49,198] [INFO] DFAST_QC result json was written to GCF_001595985.1_ASM159598v1_genomic.fna/dqc_result.json
[2024-01-24 15:32:49,198] [INFO] DFAST_QC completed!
[2024-01-24 15:32:49,198] [INFO] Total running time: 0h0m45s