[2024-01-24 11:51:09,914] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:09,916] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:09,916] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b1d085a-9572-4fb3-b585-afc13e2cf1a6/dqc_reference
[2024-01-24 11:51:11,290] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,291] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg191df142-ce17-4045-a0d7-c50465316380/GCF_014172375.1_ASM1417237v1_genomic.fna.gz | prodigal -d GCF_014172375.1_ASM1417237v1_genomic.fna/cds.fna -a GCF_014172375.1_ASM1417237v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:25,494] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:25,494] [INFO] Task started: HMMsearch
[2024-01-24 11:51:25,494] [INFO] Running command: hmmsearch --tblout GCF_014172375.1_ASM1417237v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b1d085a-9572-4fb3-b585-afc13e2cf1a6/dqc_reference/reference_markers.hmm GCF_014172375.1_ASM1417237v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:25,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:25,799] [INFO] Found 6/6 markers.
[2024-01-24 11:51:25,858] [INFO] Query marker FASTA was written to GCF_014172375.1_ASM1417237v1_genomic.fna/markers.fasta
[2024-01-24 11:51:25,859] [INFO] Task started: Blastn
[2024-01-24 11:51:25,859] [INFO] Running command: blastn -query GCF_014172375.1_ASM1417237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b1d085a-9572-4fb3-b585-afc13e2cf1a6/dqc_reference/reference_markers.fasta -out GCF_014172375.1_ASM1417237v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:26,535] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:26,539] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:26,539] [INFO] Target genome list was writen to GCF_014172375.1_ASM1417237v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:26,546] [INFO] Task started: fastANI
[2024-01-24 11:51:26,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg191df142-ce17-4045-a0d7-c50465316380/GCF_014172375.1_ASM1417237v1_genomic.fna.gz --refList GCF_014172375.1_ASM1417237v1_genomic.fna/target_genomes.txt --output GCF_014172375.1_ASM1417237v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:41,638] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:41,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b1d085a-9572-4fb3-b585-afc13e2cf1a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:41,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b1d085a-9572-4fb3-b585-afc13e2cf1a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:41,652] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:41,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:41,653] [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
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	100.0	1351	1351	95	conclusive
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	81.0067	750	1351	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	80.994	763	1351	95	below_threshold
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	80.5475	641	1351	95	below_threshold
Pedobacter namyangjuensis	strain=5G38	GCA_003313325.1	600626	600626	type	True	79.3661	535	1351	95	below_threshold
Pedobacter insulae	strain=DSM 18684	GCA_900113525.1	414048	414048	type	True	78.8748	420	1351	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	78.4479	327	1351	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	78.4294	328	1351	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	78.0788	301	1351	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	78.0767	358	1351	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	77.9735	275	1351	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	77.9594	308	1351	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	77.8213	333	1351	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.7186	253	1351	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	75.7207	51	1351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:41,654] [INFO] DFAST Taxonomy check result was written to GCF_014172375.1_ASM1417237v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:41,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:41,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:41,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b1d085a-9572-4fb3-b585-afc13e2cf1a6/dqc_reference/checkm_data
[2024-01-24 11:51:41,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:41,698] [INFO] Task started: CheckM
[2024-01-24 11:51:41,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014172375.1_ASM1417237v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014172375.1_ASM1417237v1_genomic.fna/checkm_input GCF_014172375.1_ASM1417237v1_genomic.fna/checkm_result
[2024-01-24 11:52:22,980] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:22,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:23,007] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:23,007] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:23,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014172375.1_ASM1417237v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:23,008] [INFO] Task started: Blastn
[2024-01-24 11:52:23,008] [INFO] Running command: blastn -query GCF_014172375.1_ASM1417237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b1d085a-9572-4fb3-b585-afc13e2cf1a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014172375.1_ASM1417237v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:23,813] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:23,816] [INFO] Selected 8 target genomes.
[2024-01-24 11:52:23,817] [INFO] Target genome list was writen to GCF_014172375.1_ASM1417237v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:23,822] [INFO] Task started: fastANI
[2024-01-24 11:52:23,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg191df142-ce17-4045-a0d7-c50465316380/GCF_014172375.1_ASM1417237v1_genomic.fna.gz --refList GCF_014172375.1_ASM1417237v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014172375.1_ASM1417237v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:31,823] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:31,832] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:31,832] [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_014172375.1	s__Pedobacter planticolens	100.0	1351	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013204825.1	s__Pedobacter boryungensis	85.4063	907	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331645.1	s__Pedobacter sp004331645	81.0073	761	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116505.1	s__Pedobacter sp005116505	81.0052	750	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116475.1	s__Pedobacter sp005116475	80.5278	643	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412215.1	s__Pedobacter sp001412215	80.4982	632	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377775.1	s__Pedobacter sp014377775	78.954	381	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005925345.1	s__Pedobacter ureilyticus	77.8213	333	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:31,834] [INFO] GTDB search result was written to GCF_014172375.1_ASM1417237v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:31,834] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:31,837] [INFO] DFAST_QC result json was written to GCF_014172375.1_ASM1417237v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:31,837] [INFO] DFAST_QC completed!
[2024-01-24 11:52:31,837] [INFO] Total running time: 0h1m22s