[2024-01-25 19:51:50,761] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:50,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:50,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg9be75aaa-0517-460b-a569-cab51e2e89e0/dqc_reference
[2024-01-25 19:51:51,966] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:51,966] [INFO] Task started: Prodigal
[2024-01-25 19:51:51,967] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f05261c-cb77-4044-a076-971b48324033/GCF_025821485.1_ASM2582148v1_genomic.fna.gz | prodigal -d GCF_025821485.1_ASM2582148v1_genomic.fna/cds.fna -a GCF_025821485.1_ASM2582148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:06,192] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:06,192] [INFO] Task started: HMMsearch
[2024-01-25 19:52:06,192] [INFO] Running command: hmmsearch --tblout GCF_025821485.1_ASM2582148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9be75aaa-0517-460b-a569-cab51e2e89e0/dqc_reference/reference_markers.hmm GCF_025821485.1_ASM2582148v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:06,489] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:06,490] [INFO] Found 6/6 markers.
[2024-01-25 19:52:06,542] [INFO] Query marker FASTA was written to GCF_025821485.1_ASM2582148v1_genomic.fna/markers.fasta
[2024-01-25 19:52:06,543] [INFO] Task started: Blastn
[2024-01-25 19:52:06,543] [INFO] Running command: blastn -query GCF_025821485.1_ASM2582148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9be75aaa-0517-460b-a569-cab51e2e89e0/dqc_reference/reference_markers.fasta -out GCF_025821485.1_ASM2582148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:07,634] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:07,645] [INFO] Selected 17 target genomes.
[2024-01-25 19:52:07,645] [INFO] Target genome list was writen to GCF_025821485.1_ASM2582148v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:07,661] [INFO] Task started: fastANI
[2024-01-25 19:52:07,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f05261c-cb77-4044-a076-971b48324033/GCF_025821485.1_ASM2582148v1_genomic.fna.gz --refList GCF_025821485.1_ASM2582148v1_genomic.fna/target_genomes.txt --output GCF_025821485.1_ASM2582148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:27,584] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:27,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9be75aaa-0517-460b-a569-cab51e2e89e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:27,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9be75aaa-0517-460b-a569-cab51e2e89e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:27,596] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:52:27,596] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:27,596] [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 palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	99.9142	1578	1629	95	conclusive
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	85.8121	1063	1629	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	85.8077	1073	1629	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	85.7308	1227	1629	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	84.2706	1039	1629	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	84.2119	1082	1629	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	83.7132	1113	1629	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	83.7028	995	1629	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	83.6831	1090	1629	95	below_threshold
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002219285.1	222805	1767	type	True	83.6751	1080	1629	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.634	1099	1629	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.6085	1072	1629	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	83.6014	971	1629	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	82.797	1070	1629	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	82.7727	1076	1629	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	82.2548	879	1629	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	82.1714	907	1629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:27,598] [INFO] DFAST Taxonomy check result was written to GCF_025821485.1_ASM2582148v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:27,598] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:27,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:27,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9be75aaa-0517-460b-a569-cab51e2e89e0/dqc_reference/checkm_data
[2024-01-25 19:52:27,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:27,654] [INFO] Task started: CheckM
[2024-01-25 19:52:27,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821485.1_ASM2582148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821485.1_ASM2582148v1_genomic.fna/checkm_input GCF_025821485.1_ASM2582148v1_genomic.fna/checkm_result
[2024-01-25 19:53:08,902] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:08,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:08,920] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:08,920] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:08,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821485.1_ASM2582148v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:08,921] [INFO] Task started: Blastn
[2024-01-25 19:53:08,921] [INFO] Running command: blastn -query GCF_025821485.1_ASM2582148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9be75aaa-0517-460b-a569-cab51e2e89e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821485.1_ASM2582148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:10,549] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:10,552] [INFO] Selected 15 target genomes.
[2024-01-25 19:53:10,552] [INFO] Target genome list was writen to GCF_025821485.1_ASM2582148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:10,565] [INFO] Task started: fastANI
[2024-01-25 19:53:10,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f05261c-cb77-4044-a076-971b48324033/GCF_025821485.1_ASM2582148v1_genomic.fna.gz --refList GCF_025821485.1_ASM2582148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821485.1_ASM2582148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:29,842] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:29,852] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:29,852] [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_002101785.1	s__Mycobacterium palustre	99.9142	1578	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001667035.1	s__Mycobacterium sp001667035	88.4758	1219	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730745.1	s__Mycobacterium heidelbergense	85.8008	1073	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101815.1	s__Mycobacterium paraense	85.7201	1227	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001672915.1	s__Mycobacterium sp001672915	85.5169	1161	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667015.1	s__Mycobacterium sp001667015	85.5012	1162	1629	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	85.4343	1173	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002102225.1	s__Mycobacterium interjectum_B	85.39	1200	1629	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	85.3626	1159	1629	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	85.3241	1217	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086635.1	s__Mycobacterium alsense	85.3212	1139	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_002086305.1	s__Mycobacterium malmoense_B	85.1974	1084	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_001672815.1	s__Mycobacterium sp001672815	85.1444	1154	1629	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	83.6034	1072	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_003284975.1	s__Mycobacterium europaeum_A	83.4723	1032	1629	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:29,853] [INFO] GTDB search result was written to GCF_025821485.1_ASM2582148v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:29,854] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:29,857] [INFO] DFAST_QC result json was written to GCF_025821485.1_ASM2582148v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:29,857] [INFO] DFAST_QC completed!
[2024-01-25 19:53:29,857] [INFO] Total running time: 0h1m39s