[2024-01-25 19:54:50,467] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:50,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:50,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ca809bc-1011-4d90-836a-ed06de0c5a5b/dqc_reference
[2024-01-25 19:54:51,609] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:51,609] [INFO] Task started: Prodigal
[2024-01-25 19:54:51,610] [INFO] Running command: gunzip -c /var/lib/cwl/stg4cebbf5f-e84e-4edd-b485-eb74ed8bb795/GCF_025822045.1_ASM2582204v1_genomic.fna.gz | prodigal -d GCF_025822045.1_ASM2582204v1_genomic.fna/cds.fna -a GCF_025822045.1_ASM2582204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:08,741] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:08,742] [INFO] Task started: HMMsearch
[2024-01-25 19:55:08,742] [INFO] Running command: hmmsearch --tblout GCF_025822045.1_ASM2582204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ca809bc-1011-4d90-836a-ed06de0c5a5b/dqc_reference/reference_markers.hmm GCF_025822045.1_ASM2582204v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:09,156] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:09,158] [INFO] Found 6/6 markers.
[2024-01-25 19:55:09,204] [INFO] Query marker FASTA was written to GCF_025822045.1_ASM2582204v1_genomic.fna/markers.fasta
[2024-01-25 19:55:09,204] [INFO] Task started: Blastn
[2024-01-25 19:55:09,204] [INFO] Running command: blastn -query GCF_025822045.1_ASM2582204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ca809bc-1011-4d90-836a-ed06de0c5a5b/dqc_reference/reference_markers.fasta -out GCF_025822045.1_ASM2582204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:10,346] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:10,349] [INFO] Selected 14 target genomes.
[2024-01-25 19:55:10,349] [INFO] Target genome list was writen to GCF_025822045.1_ASM2582204v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:10,364] [INFO] Task started: fastANI
[2024-01-25 19:55:10,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cebbf5f-e84e-4edd-b485-eb74ed8bb795/GCF_025822045.1_ASM2582204v1_genomic.fna.gz --refList GCF_025822045.1_ASM2582204v1_genomic.fna/target_genomes.txt --output GCF_025822045.1_ASM2582204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:29,070] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:29,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ca809bc-1011-4d90-836a-ed06de0c5a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:29,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ca809bc-1011-4d90-836a-ed06de0c5a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:29,080] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:29,080] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:29,080] [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 sherrisii	strain=ATCC BAA-832	GCA_002102355.1	243061	243061	type	True	99.9714	1763	1812	95	conclusive
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	89.9432	1596	1812	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	84.4266	1368	1812	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	84.3801	1377	1812	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	84.0506	1259	1812	95	below_threshold
Mycobacterium florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	84.0445	1389	1812	95	below_threshold
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	83.9454	1397	1812	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	83.7075	1316	1812	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	82.3521	1163	1812	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	82.2482	1181	1812	95	below_threshold
Mycobacterium shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	82.1323	1189	1812	95	below_threshold
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	82.0832	1196	1812	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	81.8166	1165	1812	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	81.3715	1082	1812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:29,082] [INFO] DFAST Taxonomy check result was written to GCF_025822045.1_ASM2582204v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:29,082] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:29,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:29,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ca809bc-1011-4d90-836a-ed06de0c5a5b/dqc_reference/checkm_data
[2024-01-25 19:55:29,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:29,136] [INFO] Task started: CheckM
[2024-01-25 19:55:29,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822045.1_ASM2582204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822045.1_ASM2582204v1_genomic.fna/checkm_input GCF_025822045.1_ASM2582204v1_genomic.fna/checkm_result
[2024-01-25 19:56:18,167] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:18,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:18,185] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:18,185] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:18,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822045.1_ASM2582204v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:18,187] [INFO] Task started: Blastn
[2024-01-25 19:56:18,187] [INFO] Running command: blastn -query GCF_025822045.1_ASM2582204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ca809bc-1011-4d90-836a-ed06de0c5a5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822045.1_ASM2582204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:19,922] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:19,925] [INFO] Selected 13 target genomes.
[2024-01-25 19:56:19,925] [INFO] Target genome list was writen to GCF_025822045.1_ASM2582204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:19,942] [INFO] Task started: fastANI
[2024-01-25 19:56:19,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cebbf5f-e84e-4edd-b485-eb74ed8bb795/GCF_025822045.1_ASM2582204v1_genomic.fna.gz --refList GCF_025822045.1_ASM2582204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822045.1_ASM2582204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:37,009] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:37,018] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:37,018] [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_002102355.1	s__Mycobacterium sherrisii	99.9714	1763	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	99.78	0.96	0.96	2	conclusive
GCF_010727605.1	s__Mycobacterium simiae	89.9476	1595	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
GCA_902168065.1	s__Mycobacterium tilburgii	87.104	940	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000689255.1	s__Mycobacterium triplex	84.3863	1375	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001665235.1	s__Mycobacterium sp001665235	84.1694	1400	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526915.1	s__Mycobacterium genavense	84.0597	1259	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730355.1	s__Mycobacterium florentinum	84.0416	1389	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001373395.1	s__Mycobacterium lentiflavum	83.6053	1343	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	82.2692	1178	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001673535.1	s__Mycobacterium sp001673535	82.0908	1110	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291465.1	s__Mycobacterium lepraemurium	81.9642	995	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	81.89	1144	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_002102155.1	s__Mycobacterium europaeum	81.7821	1135	1812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:37,020] [INFO] GTDB search result was written to GCF_025822045.1_ASM2582204v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:37,020] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:37,023] [INFO] DFAST_QC result json was written to GCF_025822045.1_ASM2582204v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:37,023] [INFO] DFAST_QC completed!
[2024-01-25 19:56:37,023] [INFO] Total running time: 0h1m47s