[2024-01-25 18:08:50,303] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:50,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:50,304] [INFO] DQC Reference Directory: /var/lib/cwl/stgef3690b3-d21d-4d47-b6e9-4a3e36f3f85e/dqc_reference
[2024-01-25 18:08:51,393] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:51,395] [INFO] Task started: Prodigal
[2024-01-25 18:08:51,395] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ebd95aa-a106-4ba4-ae23-52ab3976333b/GCF_014337155.1_ASM1433715v1_genomic.fna.gz | prodigal -d GCF_014337155.1_ASM1433715v1_genomic.fna/cds.fna -a GCF_014337155.1_ASM1433715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:58,474] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:58,474] [INFO] Task started: HMMsearch
[2024-01-25 18:08:58,475] [INFO] Running command: hmmsearch --tblout GCF_014337155.1_ASM1433715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef3690b3-d21d-4d47-b6e9-4a3e36f3f85e/dqc_reference/reference_markers.hmm GCF_014337155.1_ASM1433715v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:58,684] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:58,685] [INFO] Found 6/6 markers.
[2024-01-25 18:08:58,708] [INFO] Query marker FASTA was written to GCF_014337155.1_ASM1433715v1_genomic.fna/markers.fasta
[2024-01-25 18:08:58,709] [INFO] Task started: Blastn
[2024-01-25 18:08:58,709] [INFO] Running command: blastn -query GCF_014337155.1_ASM1433715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef3690b3-d21d-4d47-b6e9-4a3e36f3f85e/dqc_reference/reference_markers.fasta -out GCF_014337155.1_ASM1433715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:59,244] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:59,247] [INFO] Selected 21 target genomes.
[2024-01-25 18:08:59,247] [INFO] Target genome list was writen to GCF_014337155.1_ASM1433715v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:59,268] [INFO] Task started: fastANI
[2024-01-25 18:08:59,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ebd95aa-a106-4ba4-ae23-52ab3976333b/GCF_014337155.1_ASM1433715v1_genomic.fna.gz --refList GCF_014337155.1_ASM1433715v1_genomic.fna/target_genomes.txt --output GCF_014337155.1_ASM1433715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:11,697] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:11,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef3690b3-d21d-4d47-b6e9-4a3e36f3f85e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:11,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef3690b3-d21d-4d47-b6e9-4a3e36f3f85e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:11,706] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:11,706] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:11,706] [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
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	100.0	977	980	95	conclusive
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	81.7643	121	980	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	81.6437	101	980	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	81.5763	69	980	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	81.5748	117	980	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	80.9547	64	980	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	80.8957	67	980	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	80.6333	69	980	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	80.4622	81	980	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	78.846	54	980	95	below_threshold
Jutongia huaianensis	strain=NSJ-37	GCA_014384985.1	2763668	2763668	type	True	78.6727	83	980	95	below_threshold
Anaerostipes hadrus	strain=DSM 3319	GCA_000332875.2	649756	649756	type	True	78.364	55	980	95	below_threshold
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	78.2394	56	980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:11,708] [INFO] DFAST Taxonomy check result was written to GCF_014337155.1_ASM1433715v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:11,708] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:11,708] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:11,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef3690b3-d21d-4d47-b6e9-4a3e36f3f85e/dqc_reference/checkm_data
[2024-01-25 18:09:11,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:11,739] [INFO] Task started: CheckM
[2024-01-25 18:09:11,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014337155.1_ASM1433715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014337155.1_ASM1433715v1_genomic.fna/checkm_input GCF_014337155.1_ASM1433715v1_genomic.fna/checkm_result
[2024-01-25 18:09:37,205] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:37,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:37,222] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:37,222] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:37,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014337155.1_ASM1433715v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:37,223] [INFO] Task started: Blastn
[2024-01-25 18:09:37,223] [INFO] Running command: blastn -query GCF_014337155.1_ASM1433715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef3690b3-d21d-4d47-b6e9-4a3e36f3f85e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014337155.1_ASM1433715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:38,033] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:38,036] [INFO] Selected 7 target genomes.
[2024-01-25 18:09:38,036] [INFO] Target genome list was writen to GCF_014337155.1_ASM1433715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:38,042] [INFO] Task started: fastANI
[2024-01-25 18:09:38,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ebd95aa-a106-4ba4-ae23-52ab3976333b/GCF_014337155.1_ASM1433715v1_genomic.fna.gz --refList GCF_014337155.1_ASM1433715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014337155.1_ASM1433715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:42,704] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:42,710] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:42,710] [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_014337155.1	s__CAG-127 sp900319515	100.0	977	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	98.02	96.09	0.90	0.85	25	conclusive
GCA_002431865.1	s__CAG-127 sp002431865	91.6422	606	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	99.73	99.73	0.84	0.84	3	-
GCF_018918185.1	s__CAG-127 sp900539705	91.3013	746	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	97.05	96.96	0.87	0.83	4	-
GCA_002404515.1	s__CAG-127 sp002404515	90.6461	588	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553925.1	s__CAG-127 sp900553925	90.0362	466	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	97.14	96.66	0.89	0.85	4	-
GCA_900767585.1	s__CAG-127 sp900767585	88.6887	589	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938485.1	s__CAG-127 sp017938485	77.5114	95	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:42,711] [INFO] GTDB search result was written to GCF_014337155.1_ASM1433715v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:42,712] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:42,715] [INFO] DFAST_QC result json was written to GCF_014337155.1_ASM1433715v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:42,715] [INFO] DFAST_QC completed!
[2024-01-25 18:09:42,715] [INFO] Total running time: 0h0m52s