[2023-06-19 13:54:08,076] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:54:08,079] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:54:08,079] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1a8842e-2852-4d27-bbcd-0ce38573a479/dqc_reference
[2023-06-19 13:54:10,069] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:54:10,070] [INFO] Task started: Prodigal
[2023-06-19 13:54:10,070] [INFO] Running command: gunzip -c /var/lib/cwl/stg61afaf90-9cb9-45f4-ab6b-465ed9025dcd/GCA_014802425.1_ASM1480242v1_genomic.fna.gz | prodigal -d GCA_014802425.1_ASM1480242v1_genomic.fna/cds.fna -a GCA_014802425.1_ASM1480242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:54:25,704] [INFO] Task succeeded: Prodigal
[2023-06-19 13:54:25,705] [INFO] Task started: HMMsearch
[2023-06-19 13:54:25,705] [INFO] Running command: hmmsearch --tblout GCA_014802425.1_ASM1480242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1a8842e-2852-4d27-bbcd-0ce38573a479/dqc_reference/reference_markers.hmm GCA_014802425.1_ASM1480242v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:54:25,981] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:54:25,982] [INFO] Found 6/6 markers.
[2023-06-19 13:54:26,011] [INFO] Query marker FASTA was written to GCA_014802425.1_ASM1480242v1_genomic.fna/markers.fasta
[2023-06-19 13:54:26,012] [INFO] Task started: Blastn
[2023-06-19 13:54:26,012] [INFO] Running command: blastn -query GCA_014802425.1_ASM1480242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a8842e-2852-4d27-bbcd-0ce38573a479/dqc_reference/reference_markers.fasta -out GCA_014802425.1_ASM1480242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:26,688] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:26,692] [INFO] Selected 33 target genomes.
[2023-06-19 13:54:26,692] [INFO] Target genome list was writen to GCA_014802425.1_ASM1480242v1_genomic.fna/target_genomes.txt
[2023-06-19 13:54:26,698] [INFO] Task started: fastANI
[2023-06-19 13:54:26,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg61afaf90-9cb9-45f4-ab6b-465ed9025dcd/GCA_014802425.1_ASM1480242v1_genomic.fna.gz --refList GCA_014802425.1_ASM1480242v1_genomic.fna/target_genomes.txt --output GCA_014802425.1_ASM1480242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:54:43,458] [INFO] Task succeeded: fastANI
[2023-06-19 13:54:43,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1a8842e-2852-4d27-bbcd-0ce38573a479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:54:43,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1a8842e-2852-4d27-bbcd-0ce38573a479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:54:43,465] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:54:43,465] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:54:43,465] [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
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	77.3527	75	903	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.0315	89	903	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	76.3755	54	903	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	75.9695	57	903	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:54:43,471] [INFO] DFAST Taxonomy check result was written to GCA_014802425.1_ASM1480242v1_genomic.fna/tc_result.tsv
[2023-06-19 13:54:43,472] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:54:43,472] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:54:43,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1a8842e-2852-4d27-bbcd-0ce38573a479/dqc_reference/checkm_data
[2023-06-19 13:54:43,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:54:43,509] [INFO] Task started: CheckM
[2023-06-19 13:54:43,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014802425.1_ASM1480242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014802425.1_ASM1480242v1_genomic.fna/checkm_input GCA_014802425.1_ASM1480242v1_genomic.fna/checkm_result
[2023-06-19 13:55:29,306] [INFO] Task succeeded: CheckM
[2023-06-19 13:55:29,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 13:55:29,330] [INFO] ===== Completeness check finished =====
[2023-06-19 13:55:29,331] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:55:29,331] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014802425.1_ASM1480242v1_genomic.fna/markers.fasta)
[2023-06-19 13:55:29,331] [INFO] Task started: Blastn
[2023-06-19 13:55:29,332] [INFO] Running command: blastn -query GCA_014802425.1_ASM1480242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a8842e-2852-4d27-bbcd-0ce38573a479/dqc_reference/reference_markers_gtdb.fasta -out GCA_014802425.1_ASM1480242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:55:30,280] [INFO] Task succeeded: Blastn
[2023-06-19 13:55:30,285] [INFO] Selected 16 target genomes.
[2023-06-19 13:55:30,286] [INFO] Target genome list was writen to GCA_014802425.1_ASM1480242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:55:30,293] [INFO] Task started: fastANI
[2023-06-19 13:55:30,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg61afaf90-9cb9-45f4-ab6b-465ed9025dcd/GCA_014802425.1_ASM1480242v1_genomic.fna.gz --refList GCA_014802425.1_ASM1480242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014802425.1_ASM1480242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:55:37,776] [INFO] Task succeeded: fastANI
[2023-06-19 13:55:37,795] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:55:37,796] [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
GCA_014802425.1	s__CAG-485 sp014802425	100.0	902	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014801595.1	s__CAG-485 sp014801595	79.526	178	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.47	97.47	0.83	0.83	2	-
GCA_910577585.1	s__CAG-485 sp910577585	79.1213	275	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760885.1	s__CAG-485 sp900760885	78.9032	159	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802625.1	s__CAG-485 sp014802625	78.732	173	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554345.1	s__CAG-485 sp900554345	78.478	174	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.71	99.71	0.77	0.77	2	-
GCA_910584125.1	s__CAG-485 sp910584125	78.3843	217	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491945.1	s__CAG-485 sp002491945	78.128	206	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.81	98.93	0.94	0.91	9	-
GCA_905214735.1	s__CAG-485 sp905214735	77.8394	186	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588245.1	s__CAG-485 sp910588245	77.8259	145	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.72	98.72	0.89	0.89	2	-
GCA_002493515.1	s__CAG-485 sp002493515	77.7615	177	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.64	97.64	0.78	0.78	2	-
GCA_014801225.1	s__CAG-485 sp014801225	77.5575	83	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689445.1	s__M3 sp001689445	77.2473	87	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__M3	95.0	99.97	99.97	0.98	0.98	2	-
GCA_002491165.1	s__CAG-485 sp002491165	77.1162	149	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.22	96.16	0.89	0.85	9	-
GCA_014802175.1	s__CAG-485 sp014802175	77.1127	63	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.58	97.46	0.67	0.65	3	-
--------------------------------------------------------------------------------
[2023-06-19 13:55:37,798] [INFO] GTDB search result was written to GCA_014802425.1_ASM1480242v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:55:37,798] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:55:37,802] [INFO] DFAST_QC result json was written to GCA_014802425.1_ASM1480242v1_genomic.fna/dqc_result.json
[2023-06-19 13:55:37,802] [INFO] DFAST_QC completed!
[2023-06-19 13:55:37,802] [INFO] Total running time: 0h1m30s