[2024-01-25 20:21:35,597] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:35,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:35,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgaab79421-f13d-41b3-bfa9-dbcc96a47808/dqc_reference
[2024-01-25 20:21:36,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:36,716] [INFO] Task started: Prodigal
[2024-01-25 20:21:36,716] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ae08788-0983-4506-a0af-b456c816e179/GCF_017874475.1_ASM1787447v1_genomic.fna.gz | prodigal -d GCF_017874475.1_ASM1787447v1_genomic.fna/cds.fna -a GCF_017874475.1_ASM1787447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:40,284] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:40,285] [INFO] Task started: HMMsearch
[2024-01-25 20:21:40,285] [INFO] Running command: hmmsearch --tblout GCF_017874475.1_ASM1787447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaab79421-f13d-41b3-bfa9-dbcc96a47808/dqc_reference/reference_markers.hmm GCF_017874475.1_ASM1787447v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:40,478] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:40,480] [INFO] Found 6/6 markers.
[2024-01-25 20:21:40,501] [INFO] Query marker FASTA was written to GCF_017874475.1_ASM1787447v1_genomic.fna/markers.fasta
[2024-01-25 20:21:40,501] [INFO] Task started: Blastn
[2024-01-25 20:21:40,501] [INFO] Running command: blastn -query GCF_017874475.1_ASM1787447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaab79421-f13d-41b3-bfa9-dbcc96a47808/dqc_reference/reference_markers.fasta -out GCF_017874475.1_ASM1787447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:41,050] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:41,053] [INFO] Selected 7 target genomes.
[2024-01-25 20:21:41,053] [INFO] Target genome list was writen to GCF_017874475.1_ASM1787447v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:41,058] [INFO] Task started: fastANI
[2024-01-25 20:21:41,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae08788-0983-4506-a0af-b456c816e179/GCF_017874475.1_ASM1787447v1_genomic.fna.gz --refList GCF_017874475.1_ASM1787447v1_genomic.fna/target_genomes.txt --output GCF_017874475.1_ASM1787447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:44,490] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:44,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaab79421-f13d-41b3-bfa9-dbcc96a47808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:44,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaab79421-f13d-41b3-bfa9-dbcc96a47808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:44,497] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:21:44,497] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:44,498] [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
Anaerococcus degeneri	strain=DSM 29674	GCA_017874475.1	361500	361500	type	True	100.0	706	708	95	conclusive
Anaerococcus degeneri	strain=FDAARGOS_1538	GCA_020215685.1	361500	361500	type	True	99.9966	697	708	95	conclusive
Anaerococcus murdochii	strain=FDAARGOS_1460	GCA_019957155.1	411577	411577	type	True	91.629	563	708	95	below_threshold
Anaerococcus lactolyticus	strain=ATCC 51172	GCA_000156575.1	33032	33032	type	True	85.7687	519	708	95	below_threshold
Anaerococcus mediterraneensis	strain=Marseille-P2765	GCA_900128415.1	1870984	1870984	type	True	82.7145	337	708	95	below_threshold
Anaerococcus vaginimassiliensis	strain=Marseille-P4512	GCA_900626155.1	2042308	2042308	type	True	80.5088	162	708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:44,499] [INFO] DFAST Taxonomy check result was written to GCF_017874475.1_ASM1787447v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:44,500] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:44,500] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:44,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaab79421-f13d-41b3-bfa9-dbcc96a47808/dqc_reference/checkm_data
[2024-01-25 20:21:44,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:44,525] [INFO] Task started: CheckM
[2024-01-25 20:21:44,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874475.1_ASM1787447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874475.1_ASM1787447v1_genomic.fna/checkm_input GCF_017874475.1_ASM1787447v1_genomic.fna/checkm_result
[2024-01-25 20:22:01,552] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:01,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:01,570] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:01,571] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:01,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874475.1_ASM1787447v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:01,571] [INFO] Task started: Blastn
[2024-01-25 20:22:01,571] [INFO] Running command: blastn -query GCF_017874475.1_ASM1787447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaab79421-f13d-41b3-bfa9-dbcc96a47808/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874475.1_ASM1787447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:02,350] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:02,356] [INFO] Selected 10 target genomes.
[2024-01-25 20:22:02,356] [INFO] Target genome list was writen to GCF_017874475.1_ASM1787447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:02,374] [INFO] Task started: fastANI
[2024-01-25 20:22:02,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae08788-0983-4506-a0af-b456c816e179/GCF_017874475.1_ASM1787447v1_genomic.fna.gz --refList GCF_017874475.1_ASM1787447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874475.1_ASM1787447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:06,444] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:06,452] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:06,452] [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_017874475.1	s__Anaerococcus degeneri	100.0	706	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000156575.1	s__Anaerococcus lactolyticus	85.7437	521	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	97.67	97.67	0.89	0.89	2	-
GCF_900128415.1	s__Anaerococcus mediterraneensis	82.7269	334	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551095.1	s__Anaerococcus sp900551095	82.4937	234	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312365.2	s__Anaerococcus provencensis	81.6604	146	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258475.1	s__Anaerococcus sp900258475	81.6167	339	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	96.55	96.55	0.87	0.87	2	-
GCF_900626155.1	s__Anaerococcus vaginimassiliensis	80.5088	162	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	95.85	95.85	0.94	0.94	2	-
GCF_000173355.1	s__Anaerococcus hydrogenalis	79.6313	128	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	97.52	96.64	0.89	0.85	5	-
GCA_900550345.1	s__Anaerococcus sp900550345	78.4014	74	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016798225.1	s__Anaerococcus sp900541365	78.1806	103	708	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.32	99.29	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:06,453] [INFO] GTDB search result was written to GCF_017874475.1_ASM1787447v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:06,454] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:06,459] [INFO] DFAST_QC result json was written to GCF_017874475.1_ASM1787447v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:06,461] [INFO] DFAST_QC completed!
[2024-01-25 20:22:06,461] [INFO] Total running time: 0h0m31s