[2024-01-24 13:01:12,482] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,484] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,484] [INFO] DQC Reference Directory: /var/lib/cwl/stg94805ae3-d512-413c-9b6b-d520828a83c8/dqc_reference
[2024-01-24 13:01:13,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,868] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg821768d5-0d1a-4995-aa07-89defb14641e/GCF_030408715.1_ASM3040871v1_genomic.fna.gz | prodigal -d GCF_030408715.1_ASM3040871v1_genomic.fna/cds.fna -a GCF_030408715.1_ASM3040871v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:21,326] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:21,326] [INFO] Task started: HMMsearch
[2024-01-24 13:01:21,326] [INFO] Running command: hmmsearch --tblout GCF_030408715.1_ASM3040871v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94805ae3-d512-413c-9b6b-d520828a83c8/dqc_reference/reference_markers.hmm GCF_030408715.1_ASM3040871v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:21,571] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:21,573] [INFO] Found 6/6 markers.
[2024-01-24 13:01:21,600] [INFO] Query marker FASTA was written to GCF_030408715.1_ASM3040871v1_genomic.fna/markers.fasta
[2024-01-24 13:01:21,600] [INFO] Task started: Blastn
[2024-01-24 13:01:21,600] [INFO] Running command: blastn -query GCF_030408715.1_ASM3040871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94805ae3-d512-413c-9b6b-d520828a83c8/dqc_reference/reference_markers.fasta -out GCF_030408715.1_ASM3040871v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:22,649] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:22,652] [INFO] Selected 21 target genomes.
[2024-01-24 13:01:22,653] [INFO] Target genome list was writen to GCF_030408715.1_ASM3040871v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:22,660] [INFO] Task started: fastANI
[2024-01-24 13:01:22,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg821768d5-0d1a-4995-aa07-89defb14641e/GCF_030408715.1_ASM3040871v1_genomic.fna.gz --refList GCF_030408715.1_ASM3040871v1_genomic.fna/target_genomes.txt --output GCF_030408715.1_ASM3040871v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:32,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:32,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94805ae3-d512-413c-9b6b-d520828a83c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:32,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94805ae3-d512-413c-9b6b-d520828a83c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:33,013] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:33,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:33,013] [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 massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	80.1776	393	827	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	80.0705	390	827	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	79.9779	424	827	95	below_threshold
Corynebacterium singulare	strain=IBS B52218	GCA_000833575.1	161899	161899	type	True	79.9162	333	827	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	79.7962	359	827	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	79.7354	359	827	95	below_threshold
Corynebacterium minutissimum	strain=FDAARGOS_894	GCA_016027615.1	38301	38301	type	True	79.6957	326	827	95	below_threshold
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	79.6861	323	827	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	79.628	419	827	95	below_threshold
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	79.622	374	827	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	79.6203	350	827	95	below_threshold
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	79.5756	347	827	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	79.5505	374	827	95	below_threshold
Corynebacterium minutissimum	strain=NBRC 15361	GCA_001552395.1	38301	38301	type	True	79.5323	318	827	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	79.5182	344	827	95	below_threshold
Corynebacterium minutissimum	strain=ATCC 23348	GCA_000805675.1	38301	38301	type	True	79.3918	319	827	95	below_threshold
Corynebacterium yudongzhengii	strain=2183	GCA_003065405.1	2080740	2080740	type	True	79.2488	326	827	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.2475	353	827	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	79.2306	274	827	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	78.7788	289	827	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	78.6241	277	827	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:33,019] [INFO] DFAST Taxonomy check result was written to GCF_030408715.1_ASM3040871v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:33,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:33,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:33,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94805ae3-d512-413c-9b6b-d520828a83c8/dqc_reference/checkm_data
[2024-01-24 13:01:33,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:33,047] [INFO] Task started: CheckM
[2024-01-24 13:01:33,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408715.1_ASM3040871v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408715.1_ASM3040871v1_genomic.fna/checkm_input GCF_030408715.1_ASM3040871v1_genomic.fna/checkm_result
[2024-01-24 13:01:59,910] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:59,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 2.60%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:59,938] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:59,938] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:59,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408715.1_ASM3040871v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:59,939] [INFO] Task started: Blastn
[2024-01-24 13:01:59,939] [INFO] Running command: blastn -query GCF_030408715.1_ASM3040871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94805ae3-d512-413c-9b6b-d520828a83c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408715.1_ASM3040871v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:01,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:01,420] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:01,420] [INFO] Target genome list was writen to GCF_030408715.1_ASM3040871v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:01,437] [INFO] Task started: fastANI
[2024-01-24 13:02:01,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg821768d5-0d1a-4995-aa07-89defb14641e/GCF_030408715.1_ASM3040871v1_genomic.fna.gz --refList GCF_030408715.1_ASM3040871v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408715.1_ASM3040871v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:12,063] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:12,078] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:02:12,079] [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_001815935.1	s__Corynebacterium sp001815935	94.7471	728	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586215.1	s__Corynebacterium simulans	80.7004	359	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_000420605.1	s__Corynebacterium massiliense	80.1626	394	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900092335.1	s__Corynebacterium phoceense	80.0774	390	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	79.9136	364	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_000341345.1	s__Corynebacterium halotolerans	79.9057	423	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016127015.1	s__Corynebacterium aurimucosum_E	79.7321	339	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.91	96.45	0.92	0.89	6	-
GCF_013408445.1	s__Corynebacterium tuberculostearicum	79.661	357	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCF_016889765.1	s__Corynebacterium minutissimum_B	79.6212	316	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	96.19	0.95	0.91	3	-
GCA_900539985.1	s__Corynebacterium sp900539985	79.5842	294	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_001812805.1	s__Corynebacterium sp001812805	79.5523	327	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980815.1	s__Corynebacterium camporealensis	79.5357	375	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	79.5165	344	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	79.4623	347	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_003065405.1	s__Corynebacterium yudongzhengii	79.3473	327	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900411315.1	s__Corynebacterium senegalense	79.2593	350	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838985.1	s__Corynebacterium sp012838985	79.0786	291	827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003955685.1	s__Corynebacterium sp003955685	79.0547	328	827	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 13:02:12,082] [INFO] GTDB search result was written to GCF_030408715.1_ASM3040871v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:12,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:12,088] [INFO] DFAST_QC result json was written to GCF_030408715.1_ASM3040871v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:12,088] [INFO] DFAST_QC completed!
[2024-01-24 13:02:12,088] [INFO] Total running time: 0h0m60s