[2024-01-24 13:48:59,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg20aebba3-147e-43ea-b1de-e5e339359612/dqc_reference
[2024-01-24 13:49:00,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,892] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,893] [INFO] Running command: gunzip -c /var/lib/cwl/stg0efef47e-1bf7-40b0-b593-a6a43d1cec7b/GCF_002102215.1_ASM210221v1_genomic.fna.gz | prodigal -d GCF_002102215.1_ASM210221v1_genomic.fna/cds.fna -a GCF_002102215.1_ASM210221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:16,190] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:16,190] [INFO] Task started: HMMsearch
[2024-01-24 13:49:16,190] [INFO] Running command: hmmsearch --tblout GCF_002102215.1_ASM210221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20aebba3-147e-43ea-b1de-e5e339359612/dqc_reference/reference_markers.hmm GCF_002102215.1_ASM210221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:16,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:16,482] [INFO] Found 6/6 markers.
[2024-01-24 13:49:16,527] [INFO] Query marker FASTA was written to GCF_002102215.1_ASM210221v1_genomic.fna/markers.fasta
[2024-01-24 13:49:16,528] [INFO] Task started: Blastn
[2024-01-24 13:49:16,528] [INFO] Running command: blastn -query GCF_002102215.1_ASM210221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20aebba3-147e-43ea-b1de-e5e339359612/dqc_reference/reference_markers.fasta -out GCF_002102215.1_ASM210221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:17,596] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:17,599] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:17,600] [INFO] Target genome list was writen to GCF_002102215.1_ASM210221v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:17,629] [INFO] Task started: fastANI
[2024-01-24 13:49:17,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg0efef47e-1bf7-40b0-b593-a6a43d1cec7b/GCF_002102215.1_ASM210221v1_genomic.fna.gz --refList GCF_002102215.1_ASM210221v1_genomic.fna/target_genomes.txt --output GCF_002102215.1_ASM210221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:35,070] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:35,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20aebba3-147e-43ea-b1de-e5e339359612/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:35,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20aebba3-147e-43ea-b1de-e5e339359612/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:35,087] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:35,087] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:35,087] [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=DSM 44577	GCA_002102215.1	169765	169765	type	True	100.0	1524	1539	95	conclusive
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	99.9895	1530	1539	95	conclusive
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	83.4587	1077	1539	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	83.1807	1042	1539	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	83.1793	1194	1539	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	83.1635	1022	1539	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	83.0129	1182	1539	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	82.2649	1130	1539	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	82.1523	1001	1539	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	82.0407	893	1539	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	81.9247	964	1539	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	81.7205	1148	1539	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	81.3872	983	1539	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	81.3851	931	1539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:35,089] [INFO] DFAST Taxonomy check result was written to GCF_002102215.1_ASM210221v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:35,090] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:35,090] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:35,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20aebba3-147e-43ea-b1de-e5e339359612/dqc_reference/checkm_data
[2024-01-24 13:49:35,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:35,139] [INFO] Task started: CheckM
[2024-01-24 13:49:35,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002102215.1_ASM210221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002102215.1_ASM210221v1_genomic.fna/checkm_input GCF_002102215.1_ASM210221v1_genomic.fna/checkm_result
[2024-01-24 13:50:19,942] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:19,943] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:19,965] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:19,966] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:19,966] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002102215.1_ASM210221v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:19,967] [INFO] Task started: Blastn
[2024-01-24 13:50:19,967] [INFO] Running command: blastn -query GCF_002102215.1_ASM210221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20aebba3-147e-43ea-b1de-e5e339359612/dqc_reference/reference_markers_gtdb.fasta -out GCF_002102215.1_ASM210221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:21,500] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:21,504] [INFO] Selected 18 target genomes.
[2024-01-24 13:50:21,504] [INFO] Target genome list was writen to GCF_002102215.1_ASM210221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:21,597] [INFO] Task started: fastANI
[2024-01-24 13:50:21,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg0efef47e-1bf7-40b0-b593-a6a43d1cec7b/GCF_002102215.1_ASM210221v1_genomic.fna.gz --refList GCF_002102215.1_ASM210221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002102215.1_ASM210221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:44,971] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:44,991] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:44,991] [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	99.9895	1530	1539	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_002086305.1	s__Mycobacterium malmoense_B	83.3096	1025	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_010730055.1	s__Mycobacterium shinjukuense	83.2773	1128	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_010730745.1	s__Mycobacterium heidelbergense	83.1861	1042	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101845.1	s__Mycobacterium riyadhense	83.1578	1195	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_900232995.1	s__Mycobacterium simulans	83.0115	1183	1539	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	82.7803	1113	1539	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	82.5992	1046	1539	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	82.3769	984	1539	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	82.3644	990	1539	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	82.3514	999	1539	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	82.2754	1128	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_900157385.1	s__Mycobacterium terramassiliense	82.1836	1062	1539	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	82.1392	1016	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665295.1	s__Mycobacterium sp001665295	82.0825	1051	1539	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	81.9296	963	1539	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	81.7108	965	1539	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	81.3771	932	1539	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 13:50:44,993] [INFO] GTDB search result was written to GCF_002102215.1_ASM210221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:44,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:44,998] [INFO] DFAST_QC result json was written to GCF_002102215.1_ASM210221v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:44,998] [INFO] DFAST_QC completed!
[2024-01-24 13:50:44,998] [INFO] Total running time: 0h1m45s