[2023-06-19 08:27:36,403] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:27:36,405] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:27:36,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg68ded9d6-1453-4403-b125-4711ae4e5bb5/dqc_reference
[2023-06-19 08:27:37,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:27:37,619] [INFO] Task started: Prodigal
[2023-06-19 08:27:37,620] [INFO] Running command: gunzip -c /var/lib/cwl/stga57b7478-2ff4-4426-9e5c-4921cd36708c/GCA_018376715.1_ASM1837671v1_genomic.fna.gz | prodigal -d GCA_018376715.1_ASM1837671v1_genomic.fna/cds.fna -a GCA_018376715.1_ASM1837671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:27:43,813] [INFO] Task succeeded: Prodigal
[2023-06-19 08:27:43,814] [INFO] Task started: HMMsearch
[2023-06-19 08:27:43,814] [INFO] Running command: hmmsearch --tblout GCA_018376715.1_ASM1837671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68ded9d6-1453-4403-b125-4711ae4e5bb5/dqc_reference/reference_markers.hmm GCA_018376715.1_ASM1837671v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:27:44,001] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:27:44,002] [INFO] Found 6/6 markers.
[2023-06-19 08:27:44,025] [INFO] Query marker FASTA was written to GCA_018376715.1_ASM1837671v1_genomic.fna/markers.fasta
[2023-06-19 08:27:44,026] [INFO] Task started: Blastn
[2023-06-19 08:27:44,026] [INFO] Running command: blastn -query GCA_018376715.1_ASM1837671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68ded9d6-1453-4403-b125-4711ae4e5bb5/dqc_reference/reference_markers.fasta -out GCA_018376715.1_ASM1837671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:27:44,588] [INFO] Task succeeded: Blastn
[2023-06-19 08:27:44,593] [INFO] Selected 29 target genomes.
[2023-06-19 08:27:44,593] [INFO] Target genome list was writen to GCA_018376715.1_ASM1837671v1_genomic.fna/target_genomes.txt
[2023-06-19 08:27:44,596] [INFO] Task started: fastANI
[2023-06-19 08:27:44,597] [INFO] Running command: fastANI --query /var/lib/cwl/stga57b7478-2ff4-4426-9e5c-4921cd36708c/GCA_018376715.1_ASM1837671v1_genomic.fna.gz --refList GCA_018376715.1_ASM1837671v1_genomic.fna/target_genomes.txt --output GCA_018376715.1_ASM1837671v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:27:58,473] [INFO] Task succeeded: fastANI
[2023-06-19 08:27:58,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68ded9d6-1453-4403-b125-4711ae4e5bb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:27:58,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68ded9d6-1453-4403-b125-4711ae4e5bb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:27:58,489] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:27:58,489] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:27:58,489] [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
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	79.705	55	861	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.6828	56	861	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	78.2065	54	861	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	78.0215	56	861	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	77.6593	103	861	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.558	64	861	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.4883	61	861	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.4829	62	861	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.47	61	861	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	76.4028	53	861	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	76.3905	53	861	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:27:58,491] [INFO] DFAST Taxonomy check result was written to GCA_018376715.1_ASM1837671v1_genomic.fna/tc_result.tsv
[2023-06-19 08:27:58,492] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:27:58,492] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:27:58,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68ded9d6-1453-4403-b125-4711ae4e5bb5/dqc_reference/checkm_data
[2023-06-19 08:27:58,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:27:58,531] [INFO] Task started: CheckM
[2023-06-19 08:27:58,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376715.1_ASM1837671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376715.1_ASM1837671v1_genomic.fna/checkm_input GCA_018376715.1_ASM1837671v1_genomic.fna/checkm_result
[2023-06-19 08:28:22,519] [INFO] Task succeeded: CheckM
[2023-06-19 08:28:22,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:28:22,542] [INFO] ===== Completeness check finished =====
[2023-06-19 08:28:22,543] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:28:22,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376715.1_ASM1837671v1_genomic.fna/markers.fasta)
[2023-06-19 08:28:22,543] [INFO] Task started: Blastn
[2023-06-19 08:28:22,543] [INFO] Running command: blastn -query GCA_018376715.1_ASM1837671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68ded9d6-1453-4403-b125-4711ae4e5bb5/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376715.1_ASM1837671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:28:23,355] [INFO] Task succeeded: Blastn
[2023-06-19 08:28:23,358] [INFO] Selected 14 target genomes.
[2023-06-19 08:28:23,358] [INFO] Target genome list was writen to GCA_018376715.1_ASM1837671v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:28:23,361] [INFO] Task started: fastANI
[2023-06-19 08:28:23,362] [INFO] Running command: fastANI --query /var/lib/cwl/stga57b7478-2ff4-4426-9e5c-4921cd36708c/GCA_018376715.1_ASM1837671v1_genomic.fna.gz --refList GCA_018376715.1_ASM1837671v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376715.1_ASM1837671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:28:30,749] [INFO] Task succeeded: fastANI
[2023-06-19 08:28:30,757] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:28:30,757] [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_000431515.1	s__CAG-632 sp000431515	99.0101	700	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632	95.0	98.63	97.41	0.91	0.88	5	conclusive
GCA_900539185.1	s__CAG-632 sp900539185	79.8703	335	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632	95.0	98.85	98.85	0.84	0.84	2	-
GCA_002406015.1	s__CAG-632 sp002406015	78.9068	275	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632	95.0	96.80	96.71	0.87	0.85	3	-
GCA_017623675.1	s__CAG-632 sp017623675	78.6653	236	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632	95.0	97.84	97.84	0.80	0.80	2	-
GCA_910587045.1	s__CAG-632 sp910587045	78.0743	233	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461045.1	s__CAG-632 sp017461045	77.9254	156	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783585.1	s__CAG-632 sp902783585	77.3314	145	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:28:30,760] [INFO] GTDB search result was written to GCA_018376715.1_ASM1837671v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:28:30,760] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:28:30,769] [INFO] DFAST_QC result json was written to GCA_018376715.1_ASM1837671v1_genomic.fna/dqc_result.json
[2023-06-19 08:28:30,770] [INFO] DFAST_QC completed!
[2023-06-19 08:28:30,770] [INFO] Total running time: 0h0m54s