[2024-01-24 14:55:05,317] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:05,319] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:05,319] [INFO] DQC Reference Directory: /var/lib/cwl/stgac87bbbd-4b8c-445b-b0a6-38fb8d8e919a/dqc_reference
[2024-01-24 14:55:09,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,464] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,464] [INFO] Running command: gunzip -c /var/lib/cwl/stge8a9598f-adfe-4548-923b-2e9b46a0fcb0/GCF_003814005.1_ASM381400v1_genomic.fna.gz | prodigal -d GCF_003814005.1_ASM381400v1_genomic.fna/cds.fna -a GCF_003814005.1_ASM381400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:17,614] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:17,614] [INFO] Task started: HMMsearch
[2024-01-24 14:55:17,615] [INFO] Running command: hmmsearch --tblout GCF_003814005.1_ASM381400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac87bbbd-4b8c-445b-b0a6-38fb8d8e919a/dqc_reference/reference_markers.hmm GCF_003814005.1_ASM381400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:17,864] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:17,865] [INFO] Found 6/6 markers.
[2024-01-24 14:55:17,892] [INFO] Query marker FASTA was written to GCF_003814005.1_ASM381400v1_genomic.fna/markers.fasta
[2024-01-24 14:55:17,892] [INFO] Task started: Blastn
[2024-01-24 14:55:17,892] [INFO] Running command: blastn -query GCF_003814005.1_ASM381400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac87bbbd-4b8c-445b-b0a6-38fb8d8e919a/dqc_reference/reference_markers.fasta -out GCF_003814005.1_ASM381400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:18,664] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:18,669] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:18,670] [INFO] Target genome list was writen to GCF_003814005.1_ASM381400v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:18,676] [INFO] Task started: fastANI
[2024-01-24 14:55:18,676] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a9598f-adfe-4548-923b-2e9b46a0fcb0/GCF_003814005.1_ASM381400v1_genomic.fna.gz --refList GCF_003814005.1_ASM381400v1_genomic.fna/target_genomes.txt --output GCF_003814005.1_ASM381400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:25,694] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:25,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac87bbbd-4b8c-445b-b0a6-38fb8d8e919a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:25,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac87bbbd-4b8c-445b-b0a6-38fb8d8e919a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:25,708] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:25,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:25,709] [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 pseudopelargi	strain=812CH	GCA_003814005.1	2080757	2080757	type	True	100.0	781	782	95	conclusive
Corynebacterium pelargi	strain=136/3	GCA_004114895.1	1471400	1471400	type	True	89.7539	705	782	95	below_threshold
Corynebacterium pelargi	strain=CCM 8517	GCA_014635485.1	1471400	1471400	type	True	89.5625	708	782	95	below_threshold
Corynebacterium gerontici	strain=W8	GCA_003813985.1	2079234	2079234	type	True	82.2533	436	782	95	below_threshold
Corynebacterium ulcerans	strain=NCTC7910	GCA_900187135.1	65058	65058	type	True	79.1386	112	782	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.7189	199	782	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.5021	155	782	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.247	147	782	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	78.1577	121	782	95	below_threshold
Corynebacterium silvaticum	strain=KL0182	GCA_004382825.2	2320431	2320431	type	True	78.1238	112	782	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	77.957	129	782	95	below_threshold
Corynebacterium godavarianum	strain=PRD07	GCA_016785885.1	2054421	2054421	type	True	77.8236	109	782	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	77.476	108	782	95	below_threshold
Corynebacterium lowii	strain=NML 130206	GCA_001412085.1	1544413	1544413	type	True	77.3628	147	782	95	below_threshold
Corynebacterium hadale	strain=NBT06-6	GCA_002273005.1	2026255	2026255	type	True	77.2692	110	782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:25,710] [INFO] DFAST Taxonomy check result was written to GCF_003814005.1_ASM381400v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:25,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:25,711] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:25,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac87bbbd-4b8c-445b-b0a6-38fb8d8e919a/dqc_reference/checkm_data
[2024-01-24 14:55:25,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:25,736] [INFO] Task started: CheckM
[2024-01-24 14:55:25,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003814005.1_ASM381400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003814005.1_ASM381400v1_genomic.fna/checkm_input GCF_003814005.1_ASM381400v1_genomic.fna/checkm_result
[2024-01-24 14:55:55,176] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:55,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:55,195] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:55,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:55,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003814005.1_ASM381400v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:55,196] [INFO] Task started: Blastn
[2024-01-24 14:55:55,197] [INFO] Running command: blastn -query GCF_003814005.1_ASM381400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac87bbbd-4b8c-445b-b0a6-38fb8d8e919a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003814005.1_ASM381400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:56,279] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:56,283] [INFO] Selected 16 target genomes.
[2024-01-24 14:55:56,283] [INFO] Target genome list was writen to GCF_003814005.1_ASM381400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:56,305] [INFO] Task started: fastANI
[2024-01-24 14:55:56,305] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a9598f-adfe-4548-923b-2e9b46a0fcb0/GCF_003814005.1_ASM381400v1_genomic.fna.gz --refList GCF_003814005.1_ASM381400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003814005.1_ASM381400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:04,946] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:04,958] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:04,958] [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_003814005.1	s__Corynebacterium pseudopelargi	100.0	781	782	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_004114895.1	s__Corynebacterium pelargi	89.7539	705	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003813985.1	s__Corynebacterium geronticis	82.2533	436	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187135.1	s__Corynebacterium ulcerans	79.0909	111	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	-
GCF_001457455.1	s__Corynebacterium diphtheriae	78.8244	128	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.5923	198	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_902702935.1	s__Corynebacterium rouxii	78.5792	127	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021025.1	s__Corynebacterium epidermidicanis	78.5706	111	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941445.1	s__Corynebacterium aquilae	78.4965	156	782	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	78.2445	147	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002994655.1	s__Corynebacterium sp002994655	78.1392	136	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004382825.2	s__Corynebacterium silvaticum	78.0935	113	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	77.957	129	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001412085.1	s__Corynebacterium lowii	77.3429	148	782	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 14:56:04,960] [INFO] GTDB search result was written to GCF_003814005.1_ASM381400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:04,961] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:04,965] [INFO] DFAST_QC result json was written to GCF_003814005.1_ASM381400v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:04,965] [INFO] DFAST_QC completed!
[2024-01-24 14:56:04,965] [INFO] Total running time: 0h0m60s