[2024-01-24 10:57:13,253] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,260] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd1590bf-378e-4f9f-ba53-e063f1b0caf8/dqc_reference
[2024-01-24 10:57:14,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,751] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bdd7995-46b8-4319-8c57-87d3a98b8790/GCF_005925365.1_ASM592536v1_genomic.fna.gz | prodigal -d GCF_005925365.1_ASM592536v1_genomic.fna/cds.fna -a GCF_005925365.1_ASM592536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:33,852] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:33,853] [INFO] Task started: HMMsearch
[2024-01-24 10:57:33,853] [INFO] Running command: hmmsearch --tblout GCF_005925365.1_ASM592536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd1590bf-378e-4f9f-ba53-e063f1b0caf8/dqc_reference/reference_markers.hmm GCF_005925365.1_ASM592536v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:34,218] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:34,219] [INFO] Found 6/6 markers.
[2024-01-24 10:57:34,287] [INFO] Query marker FASTA was written to GCF_005925365.1_ASM592536v1_genomic.fna/markers.fasta
[2024-01-24 10:57:34,287] [INFO] Task started: Blastn
[2024-01-24 10:57:34,287] [INFO] Running command: blastn -query GCF_005925365.1_ASM592536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd1590bf-378e-4f9f-ba53-e063f1b0caf8/dqc_reference/reference_markers.fasta -out GCF_005925365.1_ASM592536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:34,961] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:34,965] [INFO] Selected 14 target genomes.
[2024-01-24 10:57:34,965] [INFO] Target genome list was writen to GCF_005925365.1_ASM592536v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:34,971] [INFO] Task started: fastANI
[2024-01-24 10:57:34,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bdd7995-46b8-4319-8c57-87d3a98b8790/GCF_005925365.1_ASM592536v1_genomic.fna.gz --refList GCF_005925365.1_ASM592536v1_genomic.fna/target_genomes.txt --output GCF_005925365.1_ASM592536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:49,178] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:49,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd1590bf-378e-4f9f-ba53-e063f1b0caf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:49,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd1590bf-378e-4f9f-ba53-e063f1b0caf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:49,193] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:49,193] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:49,193] [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 xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	100.0	1655	1655	95	conclusive
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	99.9987	1650	1655	95	conclusive
Pedobacter helvus	strain=P-25	GCA_005925325.1	2563444	2563444	type	True	83.0655	977	1655	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	81.5521	858	1655	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_003313385.1	2233776	2233776	type	True	80.0243	726	1655	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_004025525.1	2233776	2233776	type	True	80.0116	728	1655	95	below_threshold
Pedobacter nanyangensis	strain=Q-4	GCA_003313505.1	1562389	1562389	type	True	79.4698	584	1655	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	78.0119	357	1655	95	below_threshold
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	77.8691	214	1655	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	77.467	227	1655	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.4548	118	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:49,195] [INFO] DFAST Taxonomy check result was written to GCF_005925365.1_ASM592536v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:49,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:49,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:49,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd1590bf-378e-4f9f-ba53-e063f1b0caf8/dqc_reference/checkm_data
[2024-01-24 10:57:49,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:49,251] [INFO] Task started: CheckM
[2024-01-24 10:57:49,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005925365.1_ASM592536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005925365.1_ASM592536v1_genomic.fna/checkm_input GCF_005925365.1_ASM592536v1_genomic.fna/checkm_result
[2024-01-24 10:58:43,724] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:43,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:43,744] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:43,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:43,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005925365.1_ASM592536v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:43,745] [INFO] Task started: Blastn
[2024-01-24 10:58:43,745] [INFO] Running command: blastn -query GCF_005925365.1_ASM592536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd1590bf-378e-4f9f-ba53-e063f1b0caf8/dqc_reference/reference_markers_gtdb.fasta -out GCF_005925365.1_ASM592536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:44,524] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:44,538] [INFO] Selected 9 target genomes.
[2024-01-24 10:58:44,538] [INFO] Target genome list was writen to GCF_005925365.1_ASM592536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:44,545] [INFO] Task started: fastANI
[2024-01-24 10:58:44,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bdd7995-46b8-4319-8c57-87d3a98b8790/GCF_005925365.1_ASM592536v1_genomic.fna.gz --refList GCF_005925365.1_ASM592536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005925365.1_ASM592536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:53,047] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:53,061] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:53,062] [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_900215335.1	s__Pedobacter xixiisoli	99.9987	1650	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_005925325.1	s__Pedobacter helvus	83.0655	977	1655	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	81.5463	860	1655	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	80.9728	614	1655	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	80.0134	728	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.94	95.89	0.93	0.87	3	-
GCF_003313335.1	s__Pedobacter zeaxanthinifaciens	79.6567	575	1655	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	79.4618	585	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336465.1	s__Pedobacter sp002336465	77.9953	172	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688475.1	s__Pedobacter sp003688475	77.9203	179	1655	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 10:58:53,063] [INFO] GTDB search result was written to GCF_005925365.1_ASM592536v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:53,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:53,066] [INFO] DFAST_QC result json was written to GCF_005925365.1_ASM592536v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:53,066] [INFO] DFAST_QC completed!
[2024-01-24 10:58:53,066] [INFO] Total running time: 0h1m40s