[2024-01-24 14:06:31,004] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:31,006] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:31,006] [INFO] DQC Reference Directory: /var/lib/cwl/stge3bda94c-067e-4485-a88b-37f8512ab083/dqc_reference
[2024-01-24 14:06:32,456] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:32,457] [INFO] Task started: Prodigal
[2024-01-24 14:06:32,457] [INFO] Running command: gunzip -c /var/lib/cwl/stg39ec87b1-5ff6-4b45-8d36-bb1ed9ab3f8a/GCF_910593785.1_IMT-300_genomic.fna.gz | prodigal -d GCF_910593785.1_IMT-300_genomic.fna/cds.fna -a GCF_910593785.1_IMT-300_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:40,450] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:40,450] [INFO] Task started: HMMsearch
[2024-01-24 14:06:40,451] [INFO] Running command: hmmsearch --tblout GCF_910593785.1_IMT-300_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3bda94c-067e-4485-a88b-37f8512ab083/dqc_reference/reference_markers.hmm GCF_910593785.1_IMT-300_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:40,727] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:40,728] [INFO] Found 6/6 markers.
[2024-01-24 14:06:40,755] [INFO] Query marker FASTA was written to GCF_910593785.1_IMT-300_genomic.fna/markers.fasta
[2024-01-24 14:06:40,755] [INFO] Task started: Blastn
[2024-01-24 14:06:40,755] [INFO] Running command: blastn -query GCF_910593785.1_IMT-300_genomic.fna/markers.fasta -db /var/lib/cwl/stge3bda94c-067e-4485-a88b-37f8512ab083/dqc_reference/reference_markers.fasta -out GCF_910593785.1_IMT-300_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:42,006] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:42,009] [INFO] Selected 16 target genomes.
[2024-01-24 14:06:42,010] [INFO] Target genome list was writen to GCF_910593785.1_IMT-300_genomic.fna/target_genomes.txt
[2024-01-24 14:06:42,461] [INFO] Task started: fastANI
[2024-01-24 14:06:42,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ec87b1-5ff6-4b45-8d36-bb1ed9ab3f8a/GCF_910593785.1_IMT-300_genomic.fna.gz --refList GCF_910593785.1_IMT-300_genomic.fna/target_genomes.txt --output GCF_910593785.1_IMT-300_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:53,654] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:53,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3bda94c-067e-4485-a88b-37f8512ab083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:53,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3bda94c-067e-4485-a88b-37f8512ab083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:53,671] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:53,671] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:53,672] [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
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	100.0	916	920	95	conclusive
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	81.4529	451	920	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	81.0478	431	920	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	81.0136	459	920	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	81.011	503	920	95	below_threshold
Leucobacter weissii	strain=S27	GCA_017565745.1	1983706	1983706	type	True	80.9426	462	920	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	80.8657	475	920	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	80.6244	421	920	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	80.6221	451	920	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	80.6103	456	920	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	80.5651	460	920	95	below_threshold
Leucobacter tardus	strain=K 70/01	GCA_017583045.1	501483	501483	type	True	79.3484	350	920	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3968	324	920	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.0679	265	920	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	77.9537	272	920	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.9089	249	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:53,673] [INFO] DFAST Taxonomy check result was written to GCF_910593785.1_IMT-300_genomic.fna/tc_result.tsv
[2024-01-24 14:06:53,674] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:53,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:53,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3bda94c-067e-4485-a88b-37f8512ab083/dqc_reference/checkm_data
[2024-01-24 14:06:53,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:53,706] [INFO] Task started: CheckM
[2024-01-24 14:06:53,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_910593785.1_IMT-300_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_910593785.1_IMT-300_genomic.fna/checkm_input GCF_910593785.1_IMT-300_genomic.fna/checkm_result
[2024-01-24 14:07:21,946] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:21,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:21,973] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:21,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:21,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_910593785.1_IMT-300_genomic.fna/markers.fasta)
[2024-01-24 14:07:21,974] [INFO] Task started: Blastn
[2024-01-24 14:07:21,974] [INFO] Running command: blastn -query GCF_910593785.1_IMT-300_genomic.fna/markers.fasta -db /var/lib/cwl/stge3bda94c-067e-4485-a88b-37f8512ab083/dqc_reference/reference_markers_gtdb.fasta -out GCF_910593785.1_IMT-300_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:23,880] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:23,883] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:23,883] [INFO] Target genome list was writen to GCF_910593785.1_IMT-300_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:23,898] [INFO] Task started: fastANI
[2024-01-24 14:07:23,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ec87b1-5ff6-4b45-8d36-bb1ed9ab3f8a/GCF_910593785.1_IMT-300_genomic.fna.gz --refList GCF_910593785.1_IMT-300_genomic.fna/target_genomes_gtdb.txt --output GCF_910593785.1_IMT-300_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:34,490] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:34,503] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:34,503] [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_910593785.1	s__Leucobacter sp910593785	100.0	916	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016771945.1	s__Leucobacter sulfamidivorax	81.7539	498	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421845.1	s__Leucobacter chironomi	81.4009	454	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028235.1	s__Leucobacter muris	81.0651	456	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_017565705.1	s__Leucobacter ruminantium	81.0383	432	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273835.1	s__Leucobacter celer	81.025	502	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752355.1	s__Leucobacter sp002752355	81.0202	457	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
GCF_017565745.1	s__Leucobacter weissii	80.9291	463	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016522505.1	s__Leucobacter sp016522505	80.8884	473	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980875.1	s__Leucobacter sp000980875	80.8766	429	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569785.1	s__Leucobacter sp003569785	80.7883	474	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016758175.1	s__Leucobacter zeae	80.6363	454	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102345.1	s__Leucobacter chromiiresistens	80.5653	460	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.76	99.76	0.96	0.96	2	-
GCF_016522535.1	s__Leucobacter sp016522535	80.3744	395	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003917135.1	s__Leucobacter chromiireducens_A	80.3638	422	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:34,505] [INFO] GTDB search result was written to GCF_910593785.1_IMT-300_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:34,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:34,510] [INFO] DFAST_QC result json was written to GCF_910593785.1_IMT-300_genomic.fna/dqc_result.json
[2024-01-24 14:07:34,510] [INFO] DFAST_QC completed!
[2024-01-24 14:07:34,510] [INFO] Total running time: 0h1m4s