[2024-01-24 15:02:16,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:16,130] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:16,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a99a949-9a25-4a8e-8df1-a5111f7fa7c4/dqc_reference
[2024-01-24 15:02:17,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:17,531] [INFO] Task started: Prodigal
[2024-01-24 15:02:17,532] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf2951f9-c400-4a7f-89bb-3b89ea354b6f/GCF_025821645.1_ASM2582164v1_genomic.fna.gz | prodigal -d GCF_025821645.1_ASM2582164v1_genomic.fna/cds.fna -a GCF_025821645.1_ASM2582164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:32,444] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:32,444] [INFO] Task started: HMMsearch
[2024-01-24 15:02:32,444] [INFO] Running command: hmmsearch --tblout GCF_025821645.1_ASM2582164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a99a949-9a25-4a8e-8df1-a5111f7fa7c4/dqc_reference/reference_markers.hmm GCF_025821645.1_ASM2582164v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:32,747] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:32,748] [INFO] Found 6/6 markers.
[2024-01-24 15:02:32,793] [INFO] Query marker FASTA was written to GCF_025821645.1_ASM2582164v1_genomic.fna/markers.fasta
[2024-01-24 15:02:32,793] [INFO] Task started: Blastn
[2024-01-24 15:02:32,794] [INFO] Running command: blastn -query GCF_025821645.1_ASM2582164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a99a949-9a25-4a8e-8df1-a5111f7fa7c4/dqc_reference/reference_markers.fasta -out GCF_025821645.1_ASM2582164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:33,890] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:33,896] [INFO] Selected 14 target genomes.
[2024-01-24 15:02:33,897] [INFO] Target genome list was writen to GCF_025821645.1_ASM2582164v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:33,904] [INFO] Task started: fastANI
[2024-01-24 15:02:33,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf2951f9-c400-4a7f-89bb-3b89ea354b6f/GCF_025821645.1_ASM2582164v1_genomic.fna.gz --refList GCF_025821645.1_ASM2582164v1_genomic.fna/target_genomes.txt --output GCF_025821645.1_ASM2582164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:51,402] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:51,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a99a949-9a25-4a8e-8df1-a5111f7fa7c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:51,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a99a949-9a25-4a8e-8df1-a5111f7fa7c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:51,415] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:51,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:51,415] [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 lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	99.981	1500	1501	95	conclusive
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	99.9571	1443	1501	95	conclusive
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	83.4392	1063	1501	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	83.2452	1008	1501	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	83.2297	1168	1501	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	83.161	1037	1501	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	82.9769	1171	1501	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	82.1995	969	1501	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	82.1781	1126	1501	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	82.0742	881	1501	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	82.0007	941	1501	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	81.7928	1101	1501	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	81.3321	916	1501	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	81.3165	977	1501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:51,417] [INFO] DFAST Taxonomy check result was written to GCF_025821645.1_ASM2582164v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:51,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:51,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:51,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a99a949-9a25-4a8e-8df1-a5111f7fa7c4/dqc_reference/checkm_data
[2024-01-24 15:02:51,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:51,466] [INFO] Task started: CheckM
[2024-01-24 15:02:51,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821645.1_ASM2582164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821645.1_ASM2582164v1_genomic.fna/checkm_input GCF_025821645.1_ASM2582164v1_genomic.fna/checkm_result
[2024-01-24 15:03:38,012] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:38,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:38,039] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:38,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:38,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821645.1_ASM2582164v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:38,040] [INFO] Task started: Blastn
[2024-01-24 15:03:38,040] [INFO] Running command: blastn -query GCF_025821645.1_ASM2582164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a99a949-9a25-4a8e-8df1-a5111f7fa7c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821645.1_ASM2582164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:39,663] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:39,666] [INFO] Selected 18 target genomes.
[2024-01-24 15:03:39,666] [INFO] Target genome list was writen to GCF_025821645.1_ASM2582164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:39,693] [INFO] Task started: fastANI
[2024-01-24 15:03:39,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf2951f9-c400-4a7f-89bb-3b89ea354b6f/GCF_025821645.1_ASM2582164v1_genomic.fna.gz --refList GCF_025821645.1_ASM2582164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821645.1_ASM2582164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:02,830] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:02,844] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:02,845] [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_010731535.1	s__Mycobacterium lacus	99.981	1500	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_010730055.1	s__Mycobacterium shinjukuense	83.4105	1096	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	83.3593	1023	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_002101845.1	s__Mycobacterium riyadhense	83.235	1168	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_010730745.1	s__Mycobacterium heidelbergense	83.1571	1037	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900232995.1	s__Mycobacterium simulans	82.9714	1172	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.78	97.78	0.92	0.92	2	-
GCF_002104675.1	s__Mycobacterium decipiens	82.8355	1098	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195955.2	s__Mycobacterium tuberculosis	82.5452	1032	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
GCF_001954275.1	s__Mycobacterium sp001954275	82.4464	958	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_001954195.1	s__Mycobacterium sp001954195	82.4436	965	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.85	0.97	0.97	2	-
GCF_001667015.1	s__Mycobacterium sp001667015	82.354	982	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078675.2	s__Mycobacterium interjectum	82.187	994	1501	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	82.1794	1124	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_001665295.1	s__Mycobacterium sp001665295	82.1428	1019	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157385.1	s__Mycobacterium terramassiliense	82.1146	1046	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741445.1	s__Mycobacterium avium	81.987	943	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCF_001667115.1	s__Mycobacterium sp001667115	81.7313	955	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001053185.1	s__Mycobacterium bohemicum	81.3099	920	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:02,847] [INFO] GTDB search result was written to GCF_025821645.1_ASM2582164v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:02,847] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:02,851] [INFO] DFAST_QC result json was written to GCF_025821645.1_ASM2582164v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:02,851] [INFO] DFAST_QC completed!
[2024-01-24 15:04:02,851] [INFO] Total running time: 0h1m47s