[2024-01-24 11:51:05,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:05,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:05,686] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7cd3521-0949-4143-b3ec-363b76e00430/dqc_reference
[2024-01-24 11:51:06,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:06,947] [INFO] Task started: Prodigal
[2024-01-24 11:51:06,947] [INFO] Running command: gunzip -c /var/lib/cwl/stge5e0563b-4a9c-4938-b002-22440298fb0f/GCF_014837045.1_ASM1483704v1_genomic.fna.gz | prodigal -d GCF_014837045.1_ASM1483704v1_genomic.fna/cds.fna -a GCF_014837045.1_ASM1483704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:17,310] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:17,311] [INFO] Task started: HMMsearch
[2024-01-24 11:51:17,311] [INFO] Running command: hmmsearch --tblout GCF_014837045.1_ASM1483704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7cd3521-0949-4143-b3ec-363b76e00430/dqc_reference/reference_markers.hmm GCF_014837045.1_ASM1483704v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:17,583] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:17,586] [INFO] Found 6/6 markers.
[2024-01-24 11:51:17,619] [INFO] Query marker FASTA was written to GCF_014837045.1_ASM1483704v1_genomic.fna/markers.fasta
[2024-01-24 11:51:17,619] [INFO] Task started: Blastn
[2024-01-24 11:51:17,620] [INFO] Running command: blastn -query GCF_014837045.1_ASM1483704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7cd3521-0949-4143-b3ec-363b76e00430/dqc_reference/reference_markers.fasta -out GCF_014837045.1_ASM1483704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:18,629] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:18,633] [INFO] Selected 12 target genomes.
[2024-01-24 11:51:18,633] [INFO] Target genome list was writen to GCF_014837045.1_ASM1483704v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:18,638] [INFO] Task started: fastANI
[2024-01-24 11:51:18,638] [INFO] Running command: fastANI --query /var/lib/cwl/stge5e0563b-4a9c-4938-b002-22440298fb0f/GCF_014837045.1_ASM1483704v1_genomic.fna.gz --refList GCF_014837045.1_ASM1483704v1_genomic.fna/target_genomes.txt --output GCF_014837045.1_ASM1483704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:25,803] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:25,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7cd3521-0949-4143-b3ec-363b76e00430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:25,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7cd3521-0949-4143-b3ec-363b76e00430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:25,817] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:25,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:25,818] [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 gallinarum	strain=Sa1YVA5	GCA_014837045.1	2762214	2762214	type	True	100.0	1025	1026	95	conclusive
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	92.4533	900	1026	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	92.441	908	1026	95	below_threshold
Corynebacterium pacaense	strain=Marseille-P2417	GCA_900169525.1	1816684	1816684	type	True	79.7113	467	1026	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	79.5904	429	1026	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	79.5882	413	1026	95	below_threshold
Corynebacterium comes	strain=2019	GCA_009734405.1	2675218	2675218	type	True	79.5204	415	1026	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	79.3765	419	1026	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	79.1768	360	1026	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	79.1314	356	1026	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_011761195.1	1718	1718	type	True	79.0184	361	1026	95	below_threshold
Corynebacterium crudilactis	strain=JZ16	GCA_001643015.1	1652495	1652495	type	True	78.6625	278	1026	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:25,820] [INFO] DFAST Taxonomy check result was written to GCF_014837045.1_ASM1483704v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:25,820] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:25,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:25,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7cd3521-0949-4143-b3ec-363b76e00430/dqc_reference/checkm_data
[2024-01-24 11:51:25,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:25,854] [INFO] Task started: CheckM
[2024-01-24 11:51:25,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837045.1_ASM1483704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837045.1_ASM1483704v1_genomic.fna/checkm_input GCF_014837045.1_ASM1483704v1_genomic.fna/checkm_result
[2024-01-24 11:52:00,495] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:00,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:00,521] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:00,521] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:00,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837045.1_ASM1483704v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:00,522] [INFO] Task started: Blastn
[2024-01-24 11:52:00,522] [INFO] Running command: blastn -query GCF_014837045.1_ASM1483704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7cd3521-0949-4143-b3ec-363b76e00430/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837045.1_ASM1483704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:01,950] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:01,955] [INFO] Selected 14 target genomes.
[2024-01-24 11:52:01,956] [INFO] Target genome list was writen to GCF_014837045.1_ASM1483704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:01,968] [INFO] Task started: fastANI
[2024-01-24 11:52:01,968] [INFO] Running command: fastANI --query /var/lib/cwl/stge5e0563b-4a9c-4938-b002-22440298fb0f/GCF_014837045.1_ASM1483704v1_genomic.fna.gz --refList GCF_014837045.1_ASM1483704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837045.1_ASM1483704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:10,106] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:10,119] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:10,119] [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_014837045.1	s__Corynebacterium sp014837045	100.0	1025	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000011305.1	s__Corynebacterium efficiens	92.4383	901	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_900169525.1	s__Corynebacterium pacaense	79.7104	466	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003955685.1	s__Corynebacterium sp003955685	79.6913	445	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341345.1	s__Corynebacterium halotolerans	79.6139	427	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177745.1	s__Corynebacterium pollutisoli	79.6008	412	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_009734405.1	s__Corynebacterium sp009734405	79.5204	415	1026	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	79.3818	416	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCA_012838985.1	s__Corynebacterium sp012838985	79.2444	354	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011325.1	s__Corynebacterium glutamicum	79.1768	360	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCF_000344785.1	s__Corynebacterium callunae	79.1676	284	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002355155.1	s__Corynebacterium suranareeae	78.7286	292	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001643015.1	s__Corynebacterium crudilactis	78.6625	278	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120635.1	s__Corynebacterium intestinavium	77.449	178	1026	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 11:52:10,121] [INFO] GTDB search result was written to GCF_014837045.1_ASM1483704v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:10,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:10,126] [INFO] DFAST_QC result json was written to GCF_014837045.1_ASM1483704v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:10,127] [INFO] DFAST_QC completed!
[2024-01-24 11:52:10,127] [INFO] Total running time: 0h1m4s