[2024-01-24 11:19:55,987] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,989] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,989] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe1cc26f-39ad-4ecc-9fe3-27b1dc2699dc/dqc_reference
[2024-01-24 11:19:57,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:57,241] [INFO] Task started: Prodigal
[2024-01-24 11:19:57,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f38dcea-350c-44c4-b6e9-5355aab61c22/GCF_024919295.1_ASM2491929v1_genomic.fna.gz | prodigal -d GCF_024919295.1_ASM2491929v1_genomic.fna/cds.fna -a GCF_024919295.1_ASM2491929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:06,889] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:06,890] [INFO] Task started: HMMsearch
[2024-01-24 11:20:06,890] [INFO] Running command: hmmsearch --tblout GCF_024919295.1_ASM2491929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe1cc26f-39ad-4ecc-9fe3-27b1dc2699dc/dqc_reference/reference_markers.hmm GCF_024919295.1_ASM2491929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:07,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:07,168] [INFO] Found 6/6 markers.
[2024-01-24 11:20:07,195] [INFO] Query marker FASTA was written to GCF_024919295.1_ASM2491929v1_genomic.fna/markers.fasta
[2024-01-24 11:20:07,196] [INFO] Task started: Blastn
[2024-01-24 11:20:07,196] [INFO] Running command: blastn -query GCF_024919295.1_ASM2491929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe1cc26f-39ad-4ecc-9fe3-27b1dc2699dc/dqc_reference/reference_markers.fasta -out GCF_024919295.1_ASM2491929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:08,312] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:08,316] [INFO] Selected 6 target genomes.
[2024-01-24 11:20:08,316] [INFO] Target genome list was writen to GCF_024919295.1_ASM2491929v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:08,319] [INFO] Task started: fastANI
[2024-01-24 11:20:08,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f38dcea-350c-44c4-b6e9-5355aab61c22/GCF_024919295.1_ASM2491929v1_genomic.fna.gz --refList GCF_024919295.1_ASM2491929v1_genomic.fna/target_genomes.txt --output GCF_024919295.1_ASM2491929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:12,419] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:12,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe1cc26f-39ad-4ecc-9fe3-27b1dc2699dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:12,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe1cc26f-39ad-4ecc-9fe3-27b1dc2699dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:12,427] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:12,427] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:12,427] [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 marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	85.1774	712	1029	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	85.1635	723	1029	95	below_threshold
Corynebacterium comes	strain=2019	GCA_009734405.1	2675218	2675218	type	True	85.0627	742	1029	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	84.2215	624	1029	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	84.1645	630	1029	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	83.7886	649	1029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:12,428] [INFO] DFAST Taxonomy check result was written to GCF_024919295.1_ASM2491929v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:12,429] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:12,429] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:12,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe1cc26f-39ad-4ecc-9fe3-27b1dc2699dc/dqc_reference/checkm_data
[2024-01-24 11:20:12,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:12,464] [INFO] Task started: CheckM
[2024-01-24 11:20:12,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024919295.1_ASM2491929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024919295.1_ASM2491929v1_genomic.fna/checkm_input GCF_024919295.1_ASM2491929v1_genomic.fna/checkm_result
[2024-01-24 11:20:45,774] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:45,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:45,807] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:45,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:45,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024919295.1_ASM2491929v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:45,808] [INFO] Task started: Blastn
[2024-01-24 11:20:45,808] [INFO] Running command: blastn -query GCF_024919295.1_ASM2491929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe1cc26f-39ad-4ecc-9fe3-27b1dc2699dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_024919295.1_ASM2491929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:47,396] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:47,400] [INFO] Selected 6 target genomes.
[2024-01-24 11:20:47,400] [INFO] Target genome list was writen to GCF_024919295.1_ASM2491929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:47,406] [INFO] Task started: fastANI
[2024-01-24 11:20:47,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f38dcea-350c-44c4-b6e9-5355aab61c22/GCF_024919295.1_ASM2491929v1_genomic.fna.gz --refList GCF_024919295.1_ASM2491929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024919295.1_ASM2491929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:51,436] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:51,448] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:20:51,448] [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_003955685.1	s__Corynebacterium sp003955685	94.3538	863	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000835165.1	s__Corynebacterium marinum	85.1631	723	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_009734405.1	s__Corynebacterium sp009734405	85.077	741	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819445.1	s__Corynebacterium humireducens	84.1645	630	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_900177745.1	s__Corynebacterium pollutisoli	83.8217	646	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCA_012838985.1	s__Corynebacterium sp012838985	83.7745	526	1029	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 11:20:51,450] [INFO] GTDB search result was written to GCF_024919295.1_ASM2491929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:51,450] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:51,454] [INFO] DFAST_QC result json was written to GCF_024919295.1_ASM2491929v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:51,455] [INFO] DFAST_QC completed!
[2024-01-24 11:20:51,455] [INFO] Total running time: 0h0m55s