[2024-01-24 13:40:43,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,100] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2a2ed9e-79f9-4573-8949-7cb93a2d222b/dqc_reference
[2024-01-24 13:40:44,341] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,341] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg41bce1cf-1e7e-4cf4-af31-8b7aab272afc/GCF_000174015.1_ASM17401v1_genomic.fna.gz | prodigal -d GCF_000174015.1_ASM17401v1_genomic.fna/cds.fna -a GCF_000174015.1_ASM17401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:49,664] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:49,664] [INFO] Task started: HMMsearch
[2024-01-24 13:40:49,664] [INFO] Running command: hmmsearch --tblout GCF_000174015.1_ASM17401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2a2ed9e-79f9-4573-8949-7cb93a2d222b/dqc_reference/reference_markers.hmm GCF_000174015.1_ASM17401v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,918] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,963] [INFO] Query marker FASTA was written to GCF_000174015.1_ASM17401v1_genomic.fna/markers.fasta
[2024-01-24 13:40:49,963] [INFO] Task started: Blastn
[2024-01-24 13:40:49,963] [INFO] Running command: blastn -query GCF_000174015.1_ASM17401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2a2ed9e-79f9-4573-8949-7cb93a2d222b/dqc_reference/reference_markers.fasta -out GCF_000174015.1_ASM17401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,635] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,639] [INFO] Selected 14 target genomes.
[2024-01-24 13:40:50,639] [INFO] Target genome list was writen to GCF_000174015.1_ASM17401v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,647] [INFO] Task started: fastANI
[2024-01-24 13:40:50,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg41bce1cf-1e7e-4cf4-af31-8b7aab272afc/GCF_000174015.1_ASM17401v1_genomic.fna.gz --refList GCF_000174015.1_ASM17401v1_genomic.fna/target_genomes.txt --output GCF_000174015.1_ASM17401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:57,099] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:57,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2a2ed9e-79f9-4573-8949-7cb93a2d222b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:57,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2a2ed9e-79f9-4573-8949-7cb93a2d222b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:57,106] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:57,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:57,106] [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
Lancefieldella rimae	strain=ATCC 49626	GCA_000174015.1	1383	1383	type	True	100.0	539	539	95	conclusive
Lancefieldella rimae	strain=DSM 7090	GCA_001438885.1	1383	1383	type	True	99.9931	537	539	95	conclusive
Lancefieldella parvula	strain=DSM 20469	GCA_000024225.1	1382	1382	type	True	80.3789	123	539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:57,107] [INFO] DFAST Taxonomy check result was written to GCF_000174015.1_ASM17401v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:57,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:57,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:57,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2a2ed9e-79f9-4573-8949-7cb93a2d222b/dqc_reference/checkm_data
[2024-01-24 13:40:57,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:57,137] [INFO] Task started: CheckM
[2024-01-24 13:40:57,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000174015.1_ASM17401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000174015.1_ASM17401v1_genomic.fna/checkm_input GCF_000174015.1_ASM17401v1_genomic.fna/checkm_result
[2024-01-24 13:41:19,736] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:19,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,756] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:19,756] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:19,757] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000174015.1_ASM17401v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:19,757] [INFO] Task started: Blastn
[2024-01-24 13:41:19,757] [INFO] Running command: blastn -query GCF_000174015.1_ASM17401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2a2ed9e-79f9-4573-8949-7cb93a2d222b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000174015.1_ASM17401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:20,759] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:20,763] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:20,764] [INFO] Target genome list was writen to GCF_000174015.1_ASM17401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:20,816] [INFO] Task started: fastANI
[2024-01-24 13:41:20,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg41bce1cf-1e7e-4cf4-af31-8b7aab272afc/GCF_000174015.1_ASM17401v1_genomic.fna.gz --refList GCF_000174015.1_ASM17401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000174015.1_ASM17401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:26,681] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:26,690] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:26,690] [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_000174015.1	s__Lancefieldella rimae	100.0	539	539	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	97.37	95.29	0.92	0.87	5	conclusive
GCF_000411555.1	s__Lancefieldella sp000411555	81.5985	291	539	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	98.88	98.88	0.91	0.91	2	-
GCF_000564995.1	s__Lancefieldella sp000564995	78.2804	118	539	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.37	95.06	0.93	0.85	23	-
GCA_015259105.1	s__Lancefieldella sp015259105	78.2397	98	539	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.21	95.21	0.86	0.86	2	-
GCA_015259045.1	s__Lancefieldella sp015259045	77.8556	92	539	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.43	95.43	0.88	0.88	2	-
GCA_902373375.1	s__Lancefieldella sp902373375	77.8314	83	539	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555335.1	s__Lancefieldella sp900555335	77.7451	80	539	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015258605.1	s__Lancefieldella sp015258605	77.3225	70	539	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:26,692] [INFO] GTDB search result was written to GCF_000174015.1_ASM17401v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:26,693] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:26,696] [INFO] DFAST_QC result json was written to GCF_000174015.1_ASM17401v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:26,696] [INFO] DFAST_QC completed!
[2024-01-24 13:41:26,697] [INFO] Total running time: 0h0m44s