[2024-01-24 13:36:45,744] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5de5b09-e224-480f-98d7-cb23605c6f64/dqc_reference
[2024-01-24 13:36:47,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,076] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg752f8170-d6b8-4a7f-99f1-2636101ca5c0/GCF_014490555.1_ASM1449055v1_genomic.fna.gz | prodigal -d GCF_014490555.1_ASM1449055v1_genomic.fna/cds.fna -a GCF_014490555.1_ASM1449055v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:54,658] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:54,658] [INFO] Task started: HMMsearch
[2024-01-24 13:36:54,658] [INFO] Running command: hmmsearch --tblout GCF_014490555.1_ASM1449055v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5de5b09-e224-480f-98d7-cb23605c6f64/dqc_reference/reference_markers.hmm GCF_014490555.1_ASM1449055v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:54,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:54,859] [INFO] Found 6/6 markers.
[2024-01-24 13:36:54,880] [INFO] Query marker FASTA was written to GCF_014490555.1_ASM1449055v1_genomic.fna/markers.fasta
[2024-01-24 13:36:54,881] [INFO] Task started: Blastn
[2024-01-24 13:36:54,881] [INFO] Running command: blastn -query GCF_014490555.1_ASM1449055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5de5b09-e224-480f-98d7-cb23605c6f64/dqc_reference/reference_markers.fasta -out GCF_014490555.1_ASM1449055v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:55,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:55,947] [INFO] Selected 7 target genomes.
[2024-01-24 13:36:55,947] [INFO] Target genome list was writen to GCF_014490555.1_ASM1449055v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:55,949] [INFO] Task started: fastANI
[2024-01-24 13:36:55,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg752f8170-d6b8-4a7f-99f1-2636101ca5c0/GCF_014490555.1_ASM1449055v1_genomic.fna.gz --refList GCF_014490555.1_ASM1449055v1_genomic.fna/target_genomes.txt --output GCF_014490555.1_ASM1449055v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:59,987] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:59,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5de5b09-e224-480f-98d7-cb23605c6f64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:59,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5de5b09-e224-480f-98d7-cb23605c6f64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:59,995] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:36:59,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:59,995] [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
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	100.0	779	779	95	conclusive
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	99.9868	766	779	95	conclusive
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	84.6331	604	779	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	84.3113	581	779	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	84.1087	573	779	95	below_threshold
Corynebacterium coyleae	strain=DSM 44184	GCA_900105505.1	53374	53374	type	True	83.9631	571	779	95	below_threshold
Corynebacterium coyleae	strain=FDAARGOS 1425	GCA_019048165.1	53374	53374	type	True	83.8326	586	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:59,997] [INFO] DFAST Taxonomy check result was written to GCF_014490555.1_ASM1449055v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:59,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:59,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:59,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5de5b09-e224-480f-98d7-cb23605c6f64/dqc_reference/checkm_data
[2024-01-24 13:36:59,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:00,025] [INFO] Task started: CheckM
[2024-01-24 13:37:00,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014490555.1_ASM1449055v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014490555.1_ASM1449055v1_genomic.fna/checkm_input GCF_014490555.1_ASM1449055v1_genomic.fna/checkm_result
[2024-01-24 13:37:26,549] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:26,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:26,571] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:26,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:26,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014490555.1_ASM1449055v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:26,572] [INFO] Task started: Blastn
[2024-01-24 13:37:26,572] [INFO] Running command: blastn -query GCF_014490555.1_ASM1449055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5de5b09-e224-480f-98d7-cb23605c6f64/dqc_reference/reference_markers_gtdb.fasta -out GCF_014490555.1_ASM1449055v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:28,386] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:28,393] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:28,393] [INFO] Target genome list was writen to GCF_014490555.1_ASM1449055v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:28,399] [INFO] Task started: fastANI
[2024-01-24 13:37:28,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg752f8170-d6b8-4a7f-99f1-2636101ca5c0/GCF_014490555.1_ASM1449055v1_genomic.fna.gz --refList GCF_014490555.1_ASM1449055v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014490555.1_ASM1449055v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:32,589] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:32,596] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:32,596] [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_014490555.1	s__Corynebacterium sp014490555	100.0	779	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	conclusive
GCF_013978595.1	s__Corynebacterium haemomassiliense	84.6349	603	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351335.1	s__Corynebacterium lipophilum	84.3413	579	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807265.1	s__Corynebacterium sp001807265	84.3119	579	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCA_900156035.1	s__Corynebacterium afermentans	84.302	569	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_900105505.1	s__Corynebacterium coyleae	83.9366	570	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.88	97.68	0.93	0.91	16	-
GCF_900176865.1	s__Corynebacterium fournieri	83.8452	571	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:32,599] [INFO] GTDB search result was written to GCF_014490555.1_ASM1449055v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:32,599] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:32,602] [INFO] DFAST_QC result json was written to GCF_014490555.1_ASM1449055v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:32,602] [INFO] DFAST_QC completed!
[2024-01-24 13:37:32,602] [INFO] Total running time: 0h0m47s