[2024-01-24 12:31:34,025] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,027] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bf901d0-486f-4e95-a9fd-1d0db2ae4eb8/dqc_reference
[2024-01-24 12:31:35,404] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,405] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,405] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d46fa5b-cf5a-488f-be5c-5dd3635607f4/GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/cds.fna -a GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:41,239] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:41,240] [INFO] Task started: HMMsearch
[2024-01-24 12:31:41,240] [INFO] Running command: hmmsearch --tblout GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bf901d0-486f-4e95-a9fd-1d0db2ae4eb8/dqc_reference/reference_markers.hmm GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:41,521] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:41,523] [INFO] Found 6/6 markers.
[2024-01-24 12:31:41,554] [INFO] Query marker FASTA was written to GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:41,555] [INFO] Task started: Blastn
[2024-01-24 12:31:41,555] [INFO] Running command: blastn -query GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bf901d0-486f-4e95-a9fd-1d0db2ae4eb8/dqc_reference/reference_markers.fasta -out GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:42,220] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:42,227] [INFO] Selected 23 target genomes.
[2024-01-24 12:31:42,228] [INFO] Target genome list was writen to GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:42,239] [INFO] Task started: fastANI
[2024-01-24 12:31:42,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d46fa5b-cf5a-488f-be5c-5dd3635607f4/GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna.gz --refList GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:53,834] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:53,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bf901d0-486f-4e95-a9fd-1d0db2ae4eb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:53,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bf901d0-486f-4e95-a9fd-1d0db2ae4eb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:53,845] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:53,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:53,846] [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
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	100.0	929	930	95	conclusive
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	77.6448	56	930	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	77.4813	62	930	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	77.4368	63	930	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	77.3649	81	930	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	77.1485	50	930	95	below_threshold
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	77.1446	66	930	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	77.0804	53	930	95	below_threshold
Butyrivibrio proteoclasticus	strain=B316	GCA_000145035.1	43305	43305	type	True	76.9871	53	930	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	76.7574	57	930	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	76.5822	57	930	95	below_threshold
Butyrivibrio fibrisolvens	strain=DSM 3071	GCA_900129945.1	831	831	suspected-type	True	76.5805	55	930	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	76.4969	56	930	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:53,847] [INFO] DFAST Taxonomy check result was written to GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:31:53,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:53,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:53,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bf901d0-486f-4e95-a9fd-1d0db2ae4eb8/dqc_reference/checkm_data
[2024-01-24 12:31:53,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:53,882] [INFO] Task started: CheckM
[2024-01-24 12:31:53,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/checkm_input GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:32:17,971] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:17,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:17,994] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:17,994] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:17,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:32:17,995] [INFO] Task started: Blastn
[2024-01-24 12:32:17,995] [INFO] Running command: blastn -query GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bf901d0-486f-4e95-a9fd-1d0db2ae4eb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:19,021] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:19,025] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:19,025] [INFO] Target genome list was writen to GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:19,059] [INFO] Task started: fastANI
[2024-01-24 12:32:19,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d46fa5b-cf5a-488f-be5c-5dd3635607f4/GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna.gz --refList GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:26,413] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:26,431] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:26,432] [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
GCF_900167085.1	s__Eubacterium_Q ruminantium	100.0	929	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	99.19	98.63	0.97	0.94	6	conclusive
GCF_900108205.1	s__Eubacterium_Q ruminantium_A	80.476	327	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430325.1	s__Eubacterium_Q sp017430325	79.7168	266	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.28	98.28	0.91	0.91	2	-
GCA_000702245.1	s__Eubacterium_Q sp000702245	79.6013	252	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.40	97.61	0.92	0.88	4	-
GCA_900321215.1	s__Eubacterium_Q sp900321215	79.0896	232	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	99.10	98.50	0.87	0.75	5	-
GCA_003520105.1	s__Eubacterium_Q sp003520105	78.2965	153	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017420535.1	s__Eubacterium_Q sp017420535	78.1326	148	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017539165.1	s__Eubacterium_Q sp017539165	78.0437	124	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789175.1	s__Eubacterium_Q sp902789175	77.9332	143	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017519155.1	s__Eubacterium_Q sp017519155	77.8628	101	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548215.1	s__Coprococcus sp900548215	76.879	51	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.00	97.92	0.89	0.88	3	-
GCA_002314775.1	s__UBA1760 sp002314775	76.8666	67	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1760	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371025.1	s__Eubacterium_Q sp002371025	76.7691	97	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782695.1	s__Eubacterium_Q sp902782695	76.1687	70	930	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:26,433] [INFO] GTDB search result was written to GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:26,434] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:26,437] [INFO] DFAST_QC result json was written to GCF_900167085.1_IMG-taxon_2585428142_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:32:26,437] [INFO] DFAST_QC completed!
[2024-01-24 12:32:26,437] [INFO] Total running time: 0h0m52s