[2024-01-25 18:02:50,495] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:50,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:50,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg911b2a64-1a1d-4b5c-9577-29262103b7c4/dqc_reference
[2024-01-25 18:02:51,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:51,722] [INFO] Task started: Prodigal
[2024-01-25 18:02:51,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg15de2c57-c15d-4531-a671-3e7b6184b2a1/GCF_013307205.1_ASM1330720v1_genomic.fna.gz | prodigal -d GCF_013307205.1_ASM1330720v1_genomic.fna/cds.fna -a GCF_013307205.1_ASM1330720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:56,320] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:56,320] [INFO] Task started: HMMsearch
[2024-01-25 18:02:56,320] [INFO] Running command: hmmsearch --tblout GCF_013307205.1_ASM1330720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg911b2a64-1a1d-4b5c-9577-29262103b7c4/dqc_reference/reference_markers.hmm GCF_013307205.1_ASM1330720v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:56,535] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:56,536] [INFO] Found 6/6 markers.
[2024-01-25 18:02:56,556] [INFO] Query marker FASTA was written to GCF_013307205.1_ASM1330720v1_genomic.fna/markers.fasta
[2024-01-25 18:02:56,557] [INFO] Task started: Blastn
[2024-01-25 18:02:56,557] [INFO] Running command: blastn -query GCF_013307205.1_ASM1330720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg911b2a64-1a1d-4b5c-9577-29262103b7c4/dqc_reference/reference_markers.fasta -out GCF_013307205.1_ASM1330720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:57,109] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:57,112] [INFO] Selected 10 target genomes.
[2024-01-25 18:02:57,112] [INFO] Target genome list was writen to GCF_013307205.1_ASM1330720v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:57,115] [INFO] Task started: fastANI
[2024-01-25 18:02:57,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg15de2c57-c15d-4531-a671-3e7b6184b2a1/GCF_013307205.1_ASM1330720v1_genomic.fna.gz --refList GCF_013307205.1_ASM1330720v1_genomic.fna/target_genomes.txt --output GCF_013307205.1_ASM1330720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:01,718] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:01,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg911b2a64-1a1d-4b5c-9577-29262103b7c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:01,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg911b2a64-1a1d-4b5c-9577-29262103b7c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:01,725] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:01,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:01,726] [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 arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	100.0	696	696	95	conclusive
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	82.9514	472	696	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	82.2061	440	696	95	below_threshold
Polynucleobacter duraquae	strain=MWH-MoK4	GCA_000973625.1	1835254	1835254	type	True	82.0293	433	696	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	81.961	425	696	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	81.6958	452	696	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	80.3158	290	696	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	80.1154	294	696	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	80.099	300	696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:01,727] [INFO] DFAST Taxonomy check result was written to GCF_013307205.1_ASM1330720v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:01,727] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:01,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:01,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg911b2a64-1a1d-4b5c-9577-29262103b7c4/dqc_reference/checkm_data
[2024-01-25 18:03:01,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:01,751] [INFO] Task started: CheckM
[2024-01-25 18:03:01,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013307205.1_ASM1330720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013307205.1_ASM1330720v1_genomic.fna/checkm_input GCF_013307205.1_ASM1330720v1_genomic.fna/checkm_result
[2024-01-25 18:03:21,185] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:21,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:21,209] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:21,210] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:21,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013307205.1_ASM1330720v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:21,210] [INFO] Task started: Blastn
[2024-01-25 18:03:21,210] [INFO] Running command: blastn -query GCF_013307205.1_ASM1330720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg911b2a64-1a1d-4b5c-9577-29262103b7c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013307205.1_ASM1330720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:22,059] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:22,061] [INFO] Selected 16 target genomes.
[2024-01-25 18:03:22,062] [INFO] Target genome list was writen to GCF_013307205.1_ASM1330720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:22,072] [INFO] Task started: fastANI
[2024-01-25 18:03:22,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg15de2c57-c15d-4531-a671-3e7b6184b2a1/GCF_013307205.1_ASM1330720v1_genomic.fna.gz --refList GCF_013307205.1_ASM1330720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013307205.1_ASM1330720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:29,473] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:29,483] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:29,483] [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_013307205.1	s__Polynucleobacter asymbioticus_A	100.0	696	696	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_002206635.1	s__Polynucleobacter aenigmaticus	82.9514	472	696	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	82.7104	465	696	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	82.6908	434	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882405.1	s__Polynucleobacter sp018882405	82.6801	415	696	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	82.6077	433	696	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	82.3702	458	696	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	82.2524	422	696	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	82.2009	427	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688155.1	s__Polynucleobacter sp018688155	82.0879	432	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882365.1	s__Polynucleobacter sp018882365	82.044	458	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973625.1	s__Polynucleobacter duraquae	82.0293	433	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095175.1	s__Polynucleobacter necessarius_I	81.7437	417	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688495.1	s__Polynucleobacter sp018688495	81.6001	438	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.81	97.81	0.94	0.94	2	-
GCF_018882245.1	s__Polynucleobacter sp018882245	80.269	292	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881925.1	s__Polynucleobacter sp903880555	79.7734	258	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.10	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:29,484] [INFO] GTDB search result was written to GCF_013307205.1_ASM1330720v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:29,485] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:29,487] [INFO] DFAST_QC result json was written to GCF_013307205.1_ASM1330720v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:29,487] [INFO] DFAST_QC completed!
[2024-01-25 18:03:29,487] [INFO] Total running time: 0h0m39s