[2024-01-24 13:21:47,277] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,302] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg2205878b-d06b-4327-b0be-fc69529c1aea/dqc_reference
[2024-01-24 13:21:48,650] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,651] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,651] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cf19cb0-c42c-4a04-a55b-c340ae5aa754/GCF_015752125.1_ASM1575212v1_genomic.fna.gz | prodigal -d GCF_015752125.1_ASM1575212v1_genomic.fna/cds.fna -a GCF_015752125.1_ASM1575212v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:57,380] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:57,381] [INFO] Task started: HMMsearch
[2024-01-24 13:21:57,381] [INFO] Running command: hmmsearch --tblout GCF_015752125.1_ASM1575212v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2205878b-d06b-4327-b0be-fc69529c1aea/dqc_reference/reference_markers.hmm GCF_015752125.1_ASM1575212v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:57,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:57,638] [INFO] Found 6/6 markers.
[2024-01-24 13:21:57,681] [INFO] Query marker FASTA was written to GCF_015752125.1_ASM1575212v1_genomic.fna/markers.fasta
[2024-01-24 13:21:57,682] [INFO] Task started: Blastn
[2024-01-24 13:21:57,682] [INFO] Running command: blastn -query GCF_015752125.1_ASM1575212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2205878b-d06b-4327-b0be-fc69529c1aea/dqc_reference/reference_markers.fasta -out GCF_015752125.1_ASM1575212v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:58,573] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:58,578] [INFO] Selected 19 target genomes.
[2024-01-24 13:21:58,578] [INFO] Target genome list was writen to GCF_015752125.1_ASM1575212v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:58,598] [INFO] Task started: fastANI
[2024-01-24 13:21:58,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cf19cb0-c42c-4a04-a55b-c340ae5aa754/GCF_015752125.1_ASM1575212v1_genomic.fna.gz --refList GCF_015752125.1_ASM1575212v1_genomic.fna/target_genomes.txt --output GCF_015752125.1_ASM1575212v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:07,371] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:07,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2205878b-d06b-4327-b0be-fc69529c1aea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:07,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2205878b-d06b-4327-b0be-fc69529c1aea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:07,386] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:07,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:07,387] [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 aquatimens	strain=DSM 45632	GCA_015752125.1	1190508	1190508	type	True	100.0	840	841	95	conclusive
Corynebacterium urinipleomorphum	strain=Marseille-P2799	GCA_900155535.1	1852380	1852380	type	True	79.7517	299	841	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	79.5435	249	841	95	below_threshold
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	79.5159	223	841	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	79.5122	250	841	95	below_threshold
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	79.3345	296	841	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.1007	263	841	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	79.0345	258	841	95	below_threshold
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	78.9989	243	841	95	below_threshold
Corynebacterium riegelii	strain=FDAARGOS_1114	GCA_016728505.1	156976	156976	type	True	78.9592	215	841	95	below_threshold
Corynebacterium tuscaniense	strain=CCUG 51321T	GCA_008693065.1	302449	302449	type	True	78.8627	225	841	95	below_threshold
Corynebacterium qintianiae	strain=MC1420	GCA_011038645.2	2709392	2709392	type	True	78.4519	218	841	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.6579	182	841	95	below_threshold
Corynebacterium variabile	strain=NBRC 15286	GCA_006539825.1	1727	1727	type	True	76.9916	105	841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:07,389] [INFO] DFAST Taxonomy check result was written to GCF_015752125.1_ASM1575212v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:07,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:07,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:07,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2205878b-d06b-4327-b0be-fc69529c1aea/dqc_reference/checkm_data
[2024-01-24 13:22:07,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:07,472] [INFO] Task started: CheckM
[2024-01-24 13:22:07,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015752125.1_ASM1575212v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015752125.1_ASM1575212v1_genomic.fna/checkm_input GCF_015752125.1_ASM1575212v1_genomic.fna/checkm_result
[2024-01-24 13:22:39,700] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:39,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:39,728] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:39,729] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:39,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015752125.1_ASM1575212v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:39,729] [INFO] Task started: Blastn
[2024-01-24 13:22:39,729] [INFO] Running command: blastn -query GCF_015752125.1_ASM1575212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2205878b-d06b-4327-b0be-fc69529c1aea/dqc_reference/reference_markers_gtdb.fasta -out GCF_015752125.1_ASM1575212v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:41,028] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:41,031] [INFO] Selected 20 target genomes.
[2024-01-24 13:22:41,031] [INFO] Target genome list was writen to GCF_015752125.1_ASM1575212v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:41,052] [INFO] Task started: fastANI
[2024-01-24 13:22:41,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cf19cb0-c42c-4a04-a55b-c340ae5aa754/GCF_015752125.1_ASM1575212v1_genomic.fna.gz --refList GCF_015752125.1_ASM1575212v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015752125.1_ASM1575212v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:51,423] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:51,441] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:51,441] [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_015752125.1	s__Corynebacterium aquatimens	100.0	840	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900618065.1	s__Corynebacterium sp900618065	79.8668	309	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155535.1	s__Corynebacterium urinipleomorphum	79.7512	301	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017942225.1	s__Corynebacterium sp017942225	79.5735	291	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143825.1	s__Corynebacterium genitalium_A	79.4595	298	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103625.1	s__Corynebacterium mycetoides	79.4203	249	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156665.1	s__Corynebacterium appendicis	79.3345	296	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645305.1	s__Corynebacterium sp001764565	79.3298	254	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
GCF_900411315.1	s__Corynebacterium senegalense	79.1892	262	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	79.036	257	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007641235.1	s__Corynebacterium sanguinis	79.0044	242	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_016728505.1	s__Corynebacterium riegelii	78.953	215	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.34	97.30	0.92	0.92	4	-
GCF_008693065.1	s__Corynebacterium tuscaniense	78.8433	226	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.42	98.40	0.94	0.94	3	-
GCF_011038645.2	s__Corynebacterium qintianiae	78.5252	219	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.90	98.90	0.92	0.92	2	-
GCA_002339505.1	s__Corynebacterium sp002339505	78.3476	215	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539825.1	s__Corynebacterium variabile	76.9916	105	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.53	98.15	0.92	0.86	8	-
GCA_012838985.1	s__Corynebacterium sp012838985	76.7742	144	841	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 13:22:51,443] [INFO] GTDB search result was written to GCF_015752125.1_ASM1575212v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:51,443] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:51,447] [INFO] DFAST_QC result json was written to GCF_015752125.1_ASM1575212v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:51,447] [INFO] DFAST_QC completed!
[2024-01-24 13:22:51,447] [INFO] Total running time: 0h1m4s