[2023-06-04 17:34:33,573] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:34:33,576] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:34:33,576] [INFO] DQC Reference Directory: /var/lib/cwl/stge8bda419-01b1-494d-8e7b-0ecb4cf64597/dqc_reference
[2023-06-04 17:34:36,654] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:34:36,683] [INFO] Task started: Prodigal
[2023-06-04 17:34:36,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg797e5238-f95a-40ad-93fb-09a92c0bd7ee/GCA_004556045.1_ASM455604v1_genomic.fna.gz | prodigal -d GCA_004556045.1_ASM455604v1_genomic.fna/cds.fna -a GCA_004556045.1_ASM455604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:34:42,172] [INFO] Task succeeded: Prodigal
[2023-06-04 17:34:42,172] [INFO] Task started: HMMsearch
[2023-06-04 17:34:42,172] [INFO] Running command: hmmsearch --tblout GCA_004556045.1_ASM455604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8bda419-01b1-494d-8e7b-0ecb4cf64597/dqc_reference/reference_markers.hmm GCA_004556045.1_ASM455604v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:34:42,393] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:34:42,394] [INFO] Found 6/6 markers.
[2023-06-04 17:34:42,419] [INFO] Query marker FASTA was written to GCA_004556045.1_ASM455604v1_genomic.fna/markers.fasta
[2023-06-04 17:34:42,419] [INFO] Task started: Blastn
[2023-06-04 17:34:42,419] [INFO] Running command: blastn -query GCA_004556045.1_ASM455604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8bda419-01b1-494d-8e7b-0ecb4cf64597/dqc_reference/reference_markers.fasta -out GCA_004556045.1_ASM455604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:34:43,139] [INFO] Task succeeded: Blastn
[2023-06-04 17:34:43,143] [INFO] Selected 13 target genomes.
[2023-06-04 17:34:43,143] [INFO] Target genome list was writen to GCA_004556045.1_ASM455604v1_genomic.fna/target_genomes.txt
[2023-06-04 17:34:43,770] [INFO] Task started: fastANI
[2023-06-04 17:34:43,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg797e5238-f95a-40ad-93fb-09a92c0bd7ee/GCA_004556045.1_ASM455604v1_genomic.fna.gz --refList GCA_004556045.1_ASM455604v1_genomic.fna/target_genomes.txt --output GCA_004556045.1_ASM455604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:34:49,989] [INFO] Task succeeded: fastANI
[2023-06-04 17:34:49,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8bda419-01b1-494d-8e7b-0ecb4cf64597/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:34:49,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8bda419-01b1-494d-8e7b-0ecb4cf64597/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:34:50,000] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:34:50,000] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:34:50,000] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	80.6412	325	588	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	80.1877	262	588	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.4569	205	588	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.223	175	588	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.0137	106	588	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.7097	112	588	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.458	127	588	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.5251	73	588	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	76.2866	72	588	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.2167	54	588	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:34:50,003] [INFO] DFAST Taxonomy check result was written to GCA_004556045.1_ASM455604v1_genomic.fna/tc_result.tsv
[2023-06-04 17:34:50,004] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:34:50,004] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:34:50,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8bda419-01b1-494d-8e7b-0ecb4cf64597/dqc_reference/checkm_data
[2023-06-04 17:34:50,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:34:50,031] [INFO] Task started: CheckM
[2023-06-04 17:34:50,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004556045.1_ASM455604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004556045.1_ASM455604v1_genomic.fna/checkm_input GCA_004556045.1_ASM455604v1_genomic.fna/checkm_result
[2023-06-04 17:35:12,995] [INFO] Task succeeded: CheckM
[2023-06-04 17:35:12,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 6.44%
Strain heterogeneity: 14.29%
--------------------------------------------------------------------------------
[2023-06-04 17:35:13,023] [INFO] ===== Completeness check finished =====
[2023-06-04 17:35:13,024] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:35:13,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004556045.1_ASM455604v1_genomic.fna/markers.fasta)
[2023-06-04 17:35:13,024] [INFO] Task started: Blastn
[2023-06-04 17:35:13,024] [INFO] Running command: blastn -query GCA_004556045.1_ASM455604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8bda419-01b1-494d-8e7b-0ecb4cf64597/dqc_reference/reference_markers_gtdb.fasta -out GCA_004556045.1_ASM455604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:35:14,405] [INFO] Task succeeded: Blastn
[2023-06-04 17:35:14,410] [INFO] Selected 11 target genomes.
[2023-06-04 17:35:14,411] [INFO] Target genome list was writen to GCA_004556045.1_ASM455604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:35:14,470] [INFO] Task started: fastANI
[2023-06-04 17:35:14,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg797e5238-f95a-40ad-93fb-09a92c0bd7ee/GCA_004556045.1_ASM455604v1_genomic.fna.gz --refList GCA_004556045.1_ASM455604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004556045.1_ASM455604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:35:19,409] [INFO] Task succeeded: fastANI
[2023-06-04 17:35:19,431] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:35:19,432] [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_003487665.1	s__CAG-83 sp003487665	97.2214	436	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.43	97.11	0.80	0.74	11	conclusive
GCA_000435555.1	s__CAG-83 sp000435555	86.718	373	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.91	97.56	0.88	0.73	17	-
GCA_002438575.1	s__CAG-83 sp002438575	86.5605	299	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.62	97.62	0.77	0.77	2	-
GCA_900551995.1	s__CAG-83 sp900551995	86.1277	389	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	97.61	0.85	0.83	3	-
GCA_900551355.1	s__CAG-83 sp900551355	85.0594	311	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_900550585.1	s__CAG-83 sp900550585	84.8033	355	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_900554275.1	s__CAG-83 sp900554275	84.7068	344	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.46	96.91	0.80	0.75	4	-
GCA_900547745.1	s__CAG-83 sp900547745	84.6606	363	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_900545495.1	s__CAG-83 sp900545495	84.6024	386	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_900556015.1	s__CAG-83 sp900556015	84.3895	238	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.42	97.27	0.78	0.77	3	-
GCA_900545585.1	s__CAG-83 sp900545585	83.8737	385	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.41	98.11	0.88	0.81	5	-
--------------------------------------------------------------------------------
[2023-06-04 17:35:19,434] [INFO] GTDB search result was written to GCA_004556045.1_ASM455604v1_genomic.fna/result_gtdb.tsv
[2023-06-04 17:35:19,435] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:35:19,442] [INFO] DFAST_QC result json was written to GCA_004556045.1_ASM455604v1_genomic.fna/dqc_result.json
[2023-06-04 17:35:19,443] [INFO] DFAST_QC completed!
[2023-06-04 17:35:19,443] [INFO] Total running time: 0h0m46s