[2024-01-24 13:02:03,249] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,252] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,252] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2160001-7ca9-4d6b-912b-e5001260c0fc/dqc_reference
[2024-01-24 13:02:04,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:04,530] [INFO] Task started: Prodigal
[2024-01-24 13:02:04,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg1fea7745-669e-422d-83bb-685064eb1021/GCF_000688435.1_ASM68843v1_genomic.fna.gz | prodigal -d GCF_000688435.1_ASM68843v1_genomic.fna/cds.fna -a GCF_000688435.1_ASM68843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:13,795] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:13,795] [INFO] Task started: HMMsearch
[2024-01-24 13:02:13,795] [INFO] Running command: hmmsearch --tblout GCF_000688435.1_ASM68843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2160001-7ca9-4d6b-912b-e5001260c0fc/dqc_reference/reference_markers.hmm GCF_000688435.1_ASM68843v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:14,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:14,055] [INFO] Found 6/6 markers.
[2024-01-24 13:02:14,085] [INFO] Query marker FASTA was written to GCF_000688435.1_ASM68843v1_genomic.fna/markers.fasta
[2024-01-24 13:02:14,085] [INFO] Task started: Blastn
[2024-01-24 13:02:14,085] [INFO] Running command: blastn -query GCF_000688435.1_ASM68843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2160001-7ca9-4d6b-912b-e5001260c0fc/dqc_reference/reference_markers.fasta -out GCF_000688435.1_ASM68843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:15,303] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:15,306] [INFO] Selected 9 target genomes.
[2024-01-24 13:02:15,307] [INFO] Target genome list was writen to GCF_000688435.1_ASM68843v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:15,311] [INFO] Task started: fastANI
[2024-01-24 13:02:15,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fea7745-669e-422d-83bb-685064eb1021/GCF_000688435.1_ASM68843v1_genomic.fna.gz --refList GCF_000688435.1_ASM68843v1_genomic.fna/target_genomes.txt --output GCF_000688435.1_ASM68843v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:21,018] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:21,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2160001-7ca9-4d6b-912b-e5001260c0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:21,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2160001-7ca9-4d6b-912b-e5001260c0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:21,032] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:21,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:21,032] [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 halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	100.0	1051	1054	95	conclusive
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	99.9986	1053	1054	95	conclusive
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	82.1724	591	1054	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	82.1408	582	1054	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	82.1201	619	1054	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	80.7293	538	1054	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	80.2109	466	1054	95	below_threshold
Corynebacterium maris	strain=DSM 45190	GCA_000442645.1	575200	575200	type	True	80.2097	537	1054	95	below_threshold
Corynebacterium testudinoris	strain=DSM 44614	GCA_001021045.1	136857	136857	type	True	79.5159	415	1054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:21,034] [INFO] DFAST Taxonomy check result was written to GCF_000688435.1_ASM68843v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:21,034] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:21,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:21,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2160001-7ca9-4d6b-912b-e5001260c0fc/dqc_reference/checkm_data
[2024-01-24 13:02:21,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:21,068] [INFO] Task started: CheckM
[2024-01-24 13:02:21,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000688435.1_ASM68843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000688435.1_ASM68843v1_genomic.fna/checkm_input GCF_000688435.1_ASM68843v1_genomic.fna/checkm_result
[2024-01-24 13:02:51,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:51,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:51,954] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:51,954] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:51,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000688435.1_ASM68843v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:51,955] [INFO] Task started: Blastn
[2024-01-24 13:02:51,955] [INFO] Running command: blastn -query GCF_000688435.1_ASM68843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2160001-7ca9-4d6b-912b-e5001260c0fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000688435.1_ASM68843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:53,737] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:53,742] [INFO] Selected 10 target genomes.
[2024-01-24 13:02:53,742] [INFO] Target genome list was writen to GCF_000688435.1_ASM68843v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:53,750] [INFO] Task started: fastANI
[2024-01-24 13:02:53,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fea7745-669e-422d-83bb-685064eb1021/GCF_000688435.1_ASM68843v1_genomic.fna.gz --refList GCF_000688435.1_ASM68843v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000688435.1_ASM68843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:00,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:00,145] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:00,145] [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_000341345.1	s__Corynebacterium halotolerans	99.9986	1052	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000819445.1	s__Corynebacterium humireducens	82.1465	593	1054	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	82.1281	619	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_003955685.1	s__Corynebacterium sp003955685	81.8738	625	1054	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	81.7833	493	1054	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	81.7679	617	1054	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	81.4345	591	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941485.1	s__Corynebacterium frankenforstense	80.7175	539	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442645.1	s__Corynebacterium maris	80.2096	537	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	80.2095	466	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:00,148] [INFO] GTDB search result was written to GCF_000688435.1_ASM68843v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:00,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:00,151] [INFO] DFAST_QC result json was written to GCF_000688435.1_ASM68843v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:00,151] [INFO] DFAST_QC completed!
[2024-01-24 13:03:00,151] [INFO] Total running time: 0h0m57s