[2024-01-24 13:01:39,238] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,243] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg81b4f7f7-9e6b-4a6a-a2c0-e646cd999d04/dqc_reference
[2024-01-24 13:01:40,995] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,996] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,997] [INFO] Running command: gunzip -c /var/lib/cwl/stg01d682a1-8800-4c8e-8ed0-41251ec0ba3f/GCF_000154565.1_ASM15456v1_genomic.fna.gz | prodigal -d GCF_000154565.1_ASM15456v1_genomic.fna/cds.fna -a GCF_000154565.1_ASM15456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:51,659] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:51,659] [INFO] Task started: HMMsearch
[2024-01-24 13:01:51,659] [INFO] Running command: hmmsearch --tblout GCF_000154565.1_ASM15456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81b4f7f7-9e6b-4a6a-a2c0-e646cd999d04/dqc_reference/reference_markers.hmm GCF_000154565.1_ASM15456v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:52,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:52,037] [INFO] Found 6/6 markers.
[2024-01-24 13:01:52,081] [INFO] Query marker FASTA was written to GCF_000154565.1_ASM15456v1_genomic.fna/markers.fasta
[2024-01-24 13:01:52,082] [INFO] Task started: Blastn
[2024-01-24 13:01:52,082] [INFO] Running command: blastn -query GCF_000154565.1_ASM15456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b4f7f7-9e6b-4a6a-a2c0-e646cd999d04/dqc_reference/reference_markers.fasta -out GCF_000154565.1_ASM15456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:52,845] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:52,848] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:52,848] [INFO] Target genome list was writen to GCF_000154565.1_ASM15456v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:52,856] [INFO] Task started: fastANI
[2024-01-24 13:01:52,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg01d682a1-8800-4c8e-8ed0-41251ec0ba3f/GCF_000154565.1_ASM15456v1_genomic.fna.gz --refList GCF_000154565.1_ASM15456v1_genomic.fna/target_genomes.txt --output GCF_000154565.1_ASM15456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:05,626] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:05,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81b4f7f7-9e6b-4a6a-a2c0-e646cd999d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:05,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81b4f7f7-9e6b-4a6a-a2c0-e646cd999d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:05,633] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:05,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:05,633] [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
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	100.0	1223	1224	95	conclusive
Anaerotruncus colihominis	strain=DSM 17241	GCA_025146135.1	169435	169435	type	True	99.9687	1171	1224	95	conclusive
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	78.5917	234	1224	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	77.6044	53	1224	95	below_threshold
Marasmitruncus massiliensis	strain=Marseille-P3646	GCA_900186535.1	1944642	1944642	type	True	77.0749	102	1224	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:05,635] [INFO] DFAST Taxonomy check result was written to GCF_000154565.1_ASM15456v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:05,636] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:05,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:05,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81b4f7f7-9e6b-4a6a-a2c0-e646cd999d04/dqc_reference/checkm_data
[2024-01-24 13:02:05,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:05,688] [INFO] Task started: CheckM
[2024-01-24 13:02:05,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000154565.1_ASM15456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000154565.1_ASM15456v1_genomic.fna/checkm_input GCF_000154565.1_ASM15456v1_genomic.fna/checkm_result
[2024-01-24 13:02:41,090] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:41,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:41,115] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:41,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:41,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000154565.1_ASM15456v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:41,116] [INFO] Task started: Blastn
[2024-01-24 13:02:41,117] [INFO] Running command: blastn -query GCF_000154565.1_ASM15456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b4f7f7-9e6b-4a6a-a2c0-e646cd999d04/dqc_reference/reference_markers_gtdb.fasta -out GCF_000154565.1_ASM15456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:42,316] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:42,321] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:42,322] [INFO] Target genome list was writen to GCF_000154565.1_ASM15456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:42,335] [INFO] Task started: fastANI
[2024-01-24 13:02:42,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg01d682a1-8800-4c8e-8ed0-41251ec0ba3f/GCF_000154565.1_ASM15456v1_genomic.fna.gz --refList GCF_000154565.1_ASM15456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000154565.1_ASM15456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:51,291] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:51,304] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:51,305] [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_000154565.1	s__Anaerotruncus colihominis	100.0	1223	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.95	97.75	0.87	0.80	16	conclusive
GCF_010206195.1	s__Anaerotruncus colihominis_A	89.9629	833	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.98	98.75	0.89	0.87	3	-
GCA_014385025.1	s__Fimivivens sp014385025	80.4135	71	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fimivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014385085.1	s__Anaerotruncus sp014385085	80.1484	92	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199635.1	s__Anaerotruncus massiliensis	78.5935	235	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCF_000403395.2	s__Anaerotruncus sp000403395	78.3291	124	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.44	98.36	0.83	0.79	7	-
GCF_900078395.1	s__Anaerotruncus rubiinfantis	78.1639	174	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.23	99.21	0.89	0.86	5	-
GCF_900186535.1	s__Anaerotruncus massiliensis_A	77.0749	102	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.01	98.01	0.87	0.87	2	-
GCA_019114825.1	s__Anaerotruncus excrementipullorum	76.8089	63	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.88	99.88	0.94	0.94	2	-
GCA_018716105.1	s__Fimivivens faecavium	76.5795	56	1224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fimivivens	95.0	99.67	99.42	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:51,306] [INFO] GTDB search result was written to GCF_000154565.1_ASM15456v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:51,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:51,310] [INFO] DFAST_QC result json was written to GCF_000154565.1_ASM15456v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:51,310] [INFO] DFAST_QC completed!
[2024-01-24 13:02:51,310] [INFO] Total running time: 0h1m12s