[2023-06-28 15:03:25,897] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:03:25,900] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:03:25,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg696268b6-0836-4d9a-9e5d-62b7e44619d3/dqc_reference
[2023-06-28 15:03:27,068] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:03:27,069] [INFO] Task started: Prodigal
[2023-06-28 15:03:27,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg06c56b3e-7065-497c-919c-1703b0525a41/GCA_017621615.1_ASM1762161v1_genomic.fna.gz | prodigal -d GCA_017621615.1_ASM1762161v1_genomic.fna/cds.fna -a GCA_017621615.1_ASM1762161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:03:42,805] [INFO] Task succeeded: Prodigal
[2023-06-28 15:03:42,806] [INFO] Task started: HMMsearch
[2023-06-28 15:03:42,806] [INFO] Running command: hmmsearch --tblout GCA_017621615.1_ASM1762161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg696268b6-0836-4d9a-9e5d-62b7e44619d3/dqc_reference/reference_markers.hmm GCA_017621615.1_ASM1762161v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:03:42,985] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:03:42,987] [INFO] Found 6/6 markers.
[2023-06-28 15:03:43,011] [INFO] Query marker FASTA was written to GCA_017621615.1_ASM1762161v1_genomic.fna/markers.fasta
[2023-06-28 15:03:43,011] [INFO] Task started: Blastn
[2023-06-28 15:03:43,011] [INFO] Running command: blastn -query GCA_017621615.1_ASM1762161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg696268b6-0836-4d9a-9e5d-62b7e44619d3/dqc_reference/reference_markers.fasta -out GCA_017621615.1_ASM1762161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:03:43,589] [INFO] Task succeeded: Blastn
[2023-06-28 15:03:43,592] [INFO] Selected 33 target genomes.
[2023-06-28 15:03:43,592] [INFO] Target genome list was writen to GCA_017621615.1_ASM1762161v1_genomic.fna/target_genomes.txt
[2023-06-28 15:03:43,593] [INFO] Task started: fastANI
[2023-06-28 15:03:43,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c56b3e-7065-497c-919c-1703b0525a41/GCA_017621615.1_ASM1762161v1_genomic.fna.gz --refList GCA_017621615.1_ASM1762161v1_genomic.fna/target_genomes.txt --output GCA_017621615.1_ASM1762161v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:04:03,463] [INFO] Task succeeded: fastANI
[2023-06-28 15:04:03,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg696268b6-0836-4d9a-9e5d-62b7e44619d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:04:03,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg696268b6-0836-4d9a-9e5d-62b7e44619d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:04:03,471] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:04:03,472] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 15:04:03,472] [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
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.1748	84	925	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.7024	59	925	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	76.7024	59	925	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.1438	66	925	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	75.921	55	925	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	75.8702	54	925	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	75.8696	59	925	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:04:03,474] [INFO] DFAST Taxonomy check result was written to GCA_017621615.1_ASM1762161v1_genomic.fna/tc_result.tsv
[2023-06-28 15:04:03,474] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:04:03,474] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:04:03,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg696268b6-0836-4d9a-9e5d-62b7e44619d3/dqc_reference/checkm_data
[2023-06-28 15:04:03,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:04:03,503] [INFO] Task started: CheckM
[2023-06-28 15:04:03,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017621615.1_ASM1762161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017621615.1_ASM1762161v1_genomic.fna/checkm_input GCA_017621615.1_ASM1762161v1_genomic.fna/checkm_result
[2023-06-28 15:04:47,189] [INFO] Task succeeded: CheckM
[2023-06-28 15:04:47,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:04:47,207] [INFO] ===== Completeness check finished =====
[2023-06-28 15:04:47,208] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:04:47,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017621615.1_ASM1762161v1_genomic.fna/markers.fasta)
[2023-06-28 15:04:47,208] [INFO] Task started: Blastn
[2023-06-28 15:04:47,208] [INFO] Running command: blastn -query GCA_017621615.1_ASM1762161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg696268b6-0836-4d9a-9e5d-62b7e44619d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_017621615.1_ASM1762161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:04:48,036] [INFO] Task succeeded: Blastn
[2023-06-28 15:04:48,040] [INFO] Selected 22 target genomes.
[2023-06-28 15:04:48,040] [INFO] Target genome list was writen to GCA_017621615.1_ASM1762161v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:04:48,044] [INFO] Task started: fastANI
[2023-06-28 15:04:48,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c56b3e-7065-497c-919c-1703b0525a41/GCA_017621615.1_ASM1762161v1_genomic.fna.gz --refList GCA_017621615.1_ASM1762161v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017621615.1_ASM1762161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:04:57,825] [INFO] Task succeeded: fastANI
[2023-06-28 15:04:57,840] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 15:04:57,840] [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_002491165.1	s__CAG-485 sp002491165	96.0996	696	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.22	96.16	0.89	0.85	9	conclusive
GCA_900761855.1	s__CAG-485 sp900761855	78.0136	137	925	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_014802425.1	s__CAG-485 sp014802425	77.9456	162	925	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	77.8778	138	925	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_014867205.1	s__CAG-485 sp014867205	77.7954	149	925	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_900550645.1	s__CAG-485 sp900550645	77.69	212	925	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_910584125.1	s__CAG-485 sp910584125	77.6691	201	925	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_910573745.1	s__CAG-485 sp002361215	77.6647	132	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.35	98.98	0.93	0.87	9	-
GCA_002404675.1	s__CAG-485 sp002404675	77.64	194	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.43	98.18	0.88	0.86	3	-
GCA_900541835.1	s__CAG-485 sp900541835	77.6346	205	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.47	98.95	0.96	0.93	3	-
GCA_905214735.1	s__CAG-485 sp905214735	77.5283	143	925	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	77.4623	141	925	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_002361235.1	s__CAG-485 sp002361235	77.4034	151	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.58	98.09	0.93	0.87	10	-
GCA_905198125.1	s__CAG-485 sp905198125	77.3585	148	925	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_900760815.1	s__CAG-485 sp900760815	77.1145	113	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.28	97.28	0.85	0.85	2	-
GCA_910588245.1	s__CAG-485 sp910588245	77.0627	110	925	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_910584825.1	s__Duncaniella sp910584825	77.0386	90	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004552485.1	s__CAG-873 sp004552485	76.9472	137	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.38	99.38	0.89	0.89	2	-
GCA_910589425.1	s__CAG-485 sp910589425	76.9241	101	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:04:57,842] [INFO] GTDB search result was written to GCA_017621615.1_ASM1762161v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:04:57,843] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:04:57,847] [INFO] DFAST_QC result json was written to GCA_017621615.1_ASM1762161v1_genomic.fna/dqc_result.json
[2023-06-28 15:04:57,847] [INFO] DFAST_QC completed!
[2023-06-28 15:04:57,847] [INFO] Total running time: 0h1m32s