[2024-01-24 14:05:32,656] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:32,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:32,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg2671c7ef-d215-4f3c-90af-3c5fbf0ba997/dqc_reference
[2024-01-24 14:05:33,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:33,964] [INFO] Task started: Prodigal
[2024-01-24 14:05:33,965] [INFO] Running command: gunzip -c /var/lib/cwl/stgc19aa807-8d12-4ddf-9675-39baf6f57bd9/GCF_003313335.1_ASM331333v1_genomic.fna.gz | prodigal -d GCF_003313335.1_ASM331333v1_genomic.fna/cds.fna -a GCF_003313335.1_ASM331333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:52,243] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:52,243] [INFO] Task started: HMMsearch
[2024-01-24 14:05:52,243] [INFO] Running command: hmmsearch --tblout GCF_003313335.1_ASM331333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2671c7ef-d215-4f3c-90af-3c5fbf0ba997/dqc_reference/reference_markers.hmm GCF_003313335.1_ASM331333v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:52,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:52,532] [INFO] Found 6/6 markers.
[2024-01-24 14:05:52,571] [INFO] Query marker FASTA was written to GCF_003313335.1_ASM331333v1_genomic.fna/markers.fasta
[2024-01-24 14:05:52,572] [INFO] Task started: Blastn
[2024-01-24 14:05:52,572] [INFO] Running command: blastn -query GCF_003313335.1_ASM331333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2671c7ef-d215-4f3c-90af-3c5fbf0ba997/dqc_reference/reference_markers.fasta -out GCF_003313335.1_ASM331333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:53,235] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:53,239] [INFO] Selected 12 target genomes.
[2024-01-24 14:05:53,239] [INFO] Target genome list was writen to GCF_003313335.1_ASM331333v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:53,248] [INFO] Task started: fastANI
[2024-01-24 14:05:53,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgc19aa807-8d12-4ddf-9675-39baf6f57bd9/GCF_003313335.1_ASM331333v1_genomic.fna.gz --refList GCF_003313335.1_ASM331333v1_genomic.fna/target_genomes.txt --output GCF_003313335.1_ASM331333v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:03,641] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:03,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2671c7ef-d215-4f3c-90af-3c5fbf0ba997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:03,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2671c7ef-d215-4f3c-90af-3c5fbf0ba997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:03,652] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:03,652] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:03,652] [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 helvus	strain=P-25	GCA_005925325.1	2563444	2563444	type	True	79.7302	593	1404	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	79.7138	585	1404	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	79.7058	585	1404	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_004025525.1	2233776	2233776	type	True	79.4671	546	1404	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_003313385.1	2233776	2233776	type	True	79.4309	549	1404	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	79.3659	599	1404	95	below_threshold
Pedobacter nanyangensis	strain=Q-4	GCA_003313505.1	1562389	1562389	type	True	79.2522	533	1404	95	below_threshold
Pedobacter namyangjuensis	strain=5G38	GCA_003313325.1	600626	600626	type	True	78.0563	273	1404	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	77.7908	276	1404	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.2997	58	1404	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.2554	189	1404	95	below_threshold
Pedobacter suwonensis	strain=DSM 18130	GCA_900111825.1	332999	332999	type	True	77.1214	179	1404	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:03,654] [INFO] DFAST Taxonomy check result was written to GCF_003313335.1_ASM331333v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:03,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:03,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:03,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2671c7ef-d215-4f3c-90af-3c5fbf0ba997/dqc_reference/checkm_data
[2024-01-24 14:06:03,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:03,695] [INFO] Task started: CheckM
[2024-01-24 14:06:03,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003313335.1_ASM331333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003313335.1_ASM331333v1_genomic.fna/checkm_input GCF_003313335.1_ASM331333v1_genomic.fna/checkm_result
[2024-01-24 14:06:54,278] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:54,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,298] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:54,298] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:54,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003313335.1_ASM331333v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:54,299] [INFO] Task started: Blastn
[2024-01-24 14:06:54,299] [INFO] Running command: blastn -query GCF_003313335.1_ASM331333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2671c7ef-d215-4f3c-90af-3c5fbf0ba997/dqc_reference/reference_markers_gtdb.fasta -out GCF_003313335.1_ASM331333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:55,077] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:55,080] [INFO] Selected 8 target genomes.
[2024-01-24 14:06:55,080] [INFO] Target genome list was writen to GCF_003313335.1_ASM331333v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:55,085] [INFO] Task started: fastANI
[2024-01-24 14:06:55,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgc19aa807-8d12-4ddf-9675-39baf6f57bd9/GCF_003313335.1_ASM331333v1_genomic.fna.gz --refList GCF_003313335.1_ASM331333v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003313335.1_ASM331333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:03,558] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:03,566] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:03,567] [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_003313335.1	s__Pedobacter zeaxanthinifaciens	100.0	1402	1404	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_900215335.1	s__Pedobacter xixiisoli	79.7339	582	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005925325.1	s__Pedobacter helvus	79.7222	595	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399615.1	s__Pedobacter sp002399615	79.4372	451	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313385.1	s__Pedobacter chitinilyticus	79.4331	547	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.94	95.89	0.93	0.87	3	-
GCF_005925345.1	s__Pedobacter ureilyticus	79.3677	597	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313505.1	s__Pedobacter nanyangensis	79.2522	533	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903166585.1	s__Pedobacter sp903166585	77.2403	190	1404	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 14:07:03,569] [INFO] GTDB search result was written to GCF_003313335.1_ASM331333v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:03,570] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:03,581] [INFO] DFAST_QC result json was written to GCF_003313335.1_ASM331333v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:03,581] [INFO] DFAST_QC completed!
[2024-01-24 14:07:03,581] [INFO] Total running time: 0h1m31s