[2024-01-25 18:46:05,611] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:05,613] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:05,613] [INFO] DQC Reference Directory: /var/lib/cwl/stg696a309e-ec7d-405e-a309-49c4ace2ff98/dqc_reference
[2024-01-25 18:46:06,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:06,723] [INFO] Task started: Prodigal
[2024-01-25 18:46:06,723] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd18d25d-6721-41fe-9b67-9b941da65b2c/GCF_025821765.1_ASM2582176v1_genomic.fna.gz | prodigal -d GCF_025821765.1_ASM2582176v1_genomic.fna/cds.fna -a GCF_025821765.1_ASM2582176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:27,721] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:27,722] [INFO] Task started: HMMsearch
[2024-01-25 18:46:27,722] [INFO] Running command: hmmsearch --tblout GCF_025821765.1_ASM2582176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg696a309e-ec7d-405e-a309-49c4ace2ff98/dqc_reference/reference_markers.hmm GCF_025821765.1_ASM2582176v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:27,996] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:27,997] [INFO] Found 6/6 markers.
[2024-01-25 18:46:28,046] [INFO] Query marker FASTA was written to GCF_025821765.1_ASM2582176v1_genomic.fna/markers.fasta
[2024-01-25 18:46:28,047] [INFO] Task started: Blastn
[2024-01-25 18:46:28,047] [INFO] Running command: blastn -query GCF_025821765.1_ASM2582176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg696a309e-ec7d-405e-a309-49c4ace2ff98/dqc_reference/reference_markers.fasta -out GCF_025821765.1_ASM2582176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:29,086] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:29,089] [INFO] Selected 19 target genomes.
[2024-01-25 18:46:29,089] [INFO] Target genome list was writen to GCF_025821765.1_ASM2582176v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:29,099] [INFO] Task started: fastANI
[2024-01-25 18:46:29,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd18d25d-6721-41fe-9b67-9b941da65b2c/GCF_025821765.1_ASM2582176v1_genomic.fna.gz --refList GCF_025821765.1_ASM2582176v1_genomic.fna/target_genomes.txt --output GCF_025821765.1_ASM2582176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:52,158] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:52,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg696a309e-ec7d-405e-a309-49c4ace2ff98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:52,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg696a309e-ec7d-405e-a309-49c4ace2ff98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:52,170] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:46:52,170] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:52,170] [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 conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	99.9932	1958	1959	95	conclusive
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	99.9884	1921	1959	95	conclusive
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	83.7983	1134	1959	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	83.742	1108	1959	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	83.0042	1305	1959	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	82.7732	1181	1959	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	82.7635	1080	1959	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	82.7569	1144	1959	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	82.3431	1156	1959	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	82.3352	1170	1959	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	82.3337	1164	1959	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	82.2909	1039	1959	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	82.2139	1120	1959	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	82.1645	1189	1959	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	81.9432	1009	1959	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	81.9408	1026	1959	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	81.6137	894	1959	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	80.7788	1148	1959	95	below_threshold
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	80.7559	1149	1959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:52,171] [INFO] DFAST Taxonomy check result was written to GCF_025821765.1_ASM2582176v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:52,172] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:52,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:52,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg696a309e-ec7d-405e-a309-49c4ace2ff98/dqc_reference/checkm_data
[2024-01-25 18:46:52,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:52,229] [INFO] Task started: CheckM
[2024-01-25 18:46:52,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821765.1_ASM2582176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821765.1_ASM2582176v1_genomic.fna/checkm_input GCF_025821765.1_ASM2582176v1_genomic.fna/checkm_result
[2024-01-25 18:47:51,877] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:51,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:51,918] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:51,919] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:51,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821765.1_ASM2582176v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:51,920] [INFO] Task started: Blastn
[2024-01-25 18:47:51,920] [INFO] Running command: blastn -query GCF_025821765.1_ASM2582176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg696a309e-ec7d-405e-a309-49c4ace2ff98/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821765.1_ASM2582176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:53,463] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:53,466] [INFO] Selected 23 target genomes.
[2024-01-25 18:47:53,466] [INFO] Target genome list was writen to GCF_025821765.1_ASM2582176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:53,497] [INFO] Task started: fastANI
[2024-01-25 18:47:53,497] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd18d25d-6721-41fe-9b67-9b941da65b2c/GCF_025821765.1_ASM2582176v1_genomic.fna.gz --refList GCF_025821765.1_ASM2582176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821765.1_ASM2582176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:23,832] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:23,845] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:23,846] [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_010730195.1	s__Mycobacterium conspicuum	99.9932	1958	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_010730745.1	s__Mycobacterium heidelbergense	83.7496	1140	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001673535.1	s__Mycobacterium sp001673535	83.0939	1237	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086305.1	s__Mycobacterium malmoense_B	83.0471	1124	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_002086635.1	s__Mycobacterium alsense	82.9355	1227	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_900157385.1	s__Mycobacterium terramassiliense	82.9124	1270	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667185.1	s__Mycobacterium sp001667185	82.9096	1213	1959	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	82.8302	1254	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101785.1	s__Mycobacterium palustre	82.8066	1176	1959	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	82.7426	1146	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCF_001954275.1	s__Mycobacterium sp001954275	82.6303	1148	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	82.3431	1211	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_002102155.1	s__Mycobacterium europaeum	82.3371	1141	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_007714205.1	s__Mycobacterium helveticum	82.3034	1037	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001953985.1	s__Mycobacterium colombiense_B	82.2772	1211	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_001053185.1	s__Mycobacterium bohemicum	82.218	1120	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_001667775.1	s__Mycobacterium sp001667775	81.8922	1043	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665875.1	s__Mycobacterium sp001665875	81.7315	1106	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247635.1	s__Mycobacterium sp019247635	81.6596	1011	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665395.1	s__Mycobacterium sp001665395	81.4601	1138	1959	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	80.9812	1039	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_003614435.1	s__Mycobacterium paragordonae	80.7664	1147	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_002086275.1	s__Mycobacterium intermedium	80.388	1053	1959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.88	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:23,847] [INFO] GTDB search result was written to GCF_025821765.1_ASM2582176v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:23,847] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:23,851] [INFO] DFAST_QC result json was written to GCF_025821765.1_ASM2582176v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:23,851] [INFO] DFAST_QC completed!
[2024-01-25 18:48:23,851] [INFO] Total running time: 0h2m18s