[2024-01-25 19:08:20,587] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:20,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:20,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg52265030-cf30-4d78-89c5-70415ede59b5/dqc_reference
[2024-01-25 19:08:21,702] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:21,702] [INFO] Task started: Prodigal
[2024-01-25 19:08:21,703] [INFO] Running command: gunzip -c /var/lib/cwl/stg081d2e93-4437-491a-9497-82fb267d97fe/GCF_025821905.1_ASM2582190v1_genomic.fna.gz | prodigal -d GCF_025821905.1_ASM2582190v1_genomic.fna/cds.fna -a GCF_025821905.1_ASM2582190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:45,110] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:45,110] [INFO] Task started: HMMsearch
[2024-01-25 19:08:45,110] [INFO] Running command: hmmsearch --tblout GCF_025821905.1_ASM2582190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52265030-cf30-4d78-89c5-70415ede59b5/dqc_reference/reference_markers.hmm GCF_025821905.1_ASM2582190v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:45,422] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:45,424] [INFO] Found 6/6 markers.
[2024-01-25 19:08:45,482] [INFO] Query marker FASTA was written to GCF_025821905.1_ASM2582190v1_genomic.fna/markers.fasta
[2024-01-25 19:08:45,482] [INFO] Task started: Blastn
[2024-01-25 19:08:45,482] [INFO] Running command: blastn -query GCF_025821905.1_ASM2582190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52265030-cf30-4d78-89c5-70415ede59b5/dqc_reference/reference_markers.fasta -out GCF_025821905.1_ASM2582190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:46,517] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:46,520] [INFO] Selected 14 target genomes.
[2024-01-25 19:08:46,521] [INFO] Target genome list was writen to GCF_025821905.1_ASM2582190v1_genomic.fna/target_genomes.txt
[2024-01-25 19:08:46,530] [INFO] Task started: fastANI
[2024-01-25 19:08:46,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg081d2e93-4437-491a-9497-82fb267d97fe/GCF_025821905.1_ASM2582190v1_genomic.fna.gz --refList GCF_025821905.1_ASM2582190v1_genomic.fna/target_genomes.txt --output GCF_025821905.1_ASM2582190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:12,933] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:12,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52265030-cf30-4d78-89c5-70415ede59b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:12,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52265030-cf30-4d78-89c5-70415ede59b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:12,943] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:12,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:12,943] [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
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	99.9322	2351	2497	95	conclusive
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	86.8372	1866	2497	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	86.8088	1841	2497	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_002086545.1	1790	1790	suspected-type	True	81.724	1324	2497	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_000613245.1	1790	1790	suspected-type	True	81.627	1343	2497	95	below_threshold
Mycobacterium vicinigordonae	strain=24	GCA_013466425.1	1719132	1719132	type	True	81.1823	1229	2497	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	81.1617	1128	2497	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	80.8961	1231	2497	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	80.8575	1218	2497	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.672	1080	2497	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	80.605	948	2497	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	80.5764	1120	2497	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	80.3649	1159	2497	95	below_threshold
Mycobacterium kansasii	strain=ATCC 12478	GCA_000157895.2	1768	1768	type	True	80.2285	1147	2497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:12,944] [INFO] DFAST Taxonomy check result was written to GCF_025821905.1_ASM2582190v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:12,945] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:12,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:12,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52265030-cf30-4d78-89c5-70415ede59b5/dqc_reference/checkm_data
[2024-01-25 19:09:12,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:13,016] [INFO] Task started: CheckM
[2024-01-25 19:09:13,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821905.1_ASM2582190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821905.1_ASM2582190v1_genomic.fna/checkm_input GCF_025821905.1_ASM2582190v1_genomic.fna/checkm_result
[2024-01-25 19:10:19,160] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:19,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:19,181] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:19,181] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:19,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821905.1_ASM2582190v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:19,182] [INFO] Task started: Blastn
[2024-01-25 19:10:19,182] [INFO] Running command: blastn -query GCF_025821905.1_ASM2582190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52265030-cf30-4d78-89c5-70415ede59b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821905.1_ASM2582190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:20,695] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:20,702] [INFO] Selected 10 target genomes.
[2024-01-25 19:10:20,702] [INFO] Target genome list was writen to GCF_025821905.1_ASM2582190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:20,716] [INFO] Task started: fastANI
[2024-01-25 19:10:20,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg081d2e93-4437-491a-9497-82fb267d97fe/GCF_025821905.1_ASM2582190v1_genomic.fna.gz --refList GCF_025821905.1_ASM2582190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821905.1_ASM2582190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:43,764] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:43,771] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:43,771] [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_002101675.1	s__Mycobacterium gordonae	99.9322	2351	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	conclusive
GCF_017086405.1	s__Mycobacterium gordonae_D	87.7104	1871	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417955.2	s__Mycobacterium gordonae_B	87.3302	1817	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614435.1	s__Mycobacterium paragordonae	86.8189	1868	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCA_003987775.1	s__Mycobacterium sp003987775	86.1339	1817	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466425.1	s__Mycobacterium vicinigordonae	81.1685	1233	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002116635.1	s__Mycobacterium szulgai	80.901	1231	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086155.1	s__Mycobacterium angelicum	80.8739	1220	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705925.1	s__Mycobacterium ostraviense	80.3604	1162	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_010723575.1	s__Mycobacterium bourgelatii	80.322	1278	2497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:43,773] [INFO] GTDB search result was written to GCF_025821905.1_ASM2582190v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:43,773] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:43,776] [INFO] DFAST_QC result json was written to GCF_025821905.1_ASM2582190v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:43,776] [INFO] DFAST_QC completed!
[2024-01-25 19:10:43,776] [INFO] Total running time: 0h2m23s