[2024-01-25 19:40:05,505] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:05,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:05,513] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5e6b916-3cce-4d7c-a9b7-082bb9efd2ea/dqc_reference
[2024-01-25 19:40:06,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:06,662] [INFO] Task started: Prodigal
[2024-01-25 19:40:06,662] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ff4cd01-d12b-41c5-98cf-3308e44c4f19/GCF_900292015.1_MB901379_genomic.fna.gz | prodigal -d GCF_900292015.1_MB901379_genomic.fna/cds.fna -a GCF_900292015.1_MB901379_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:47,419] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:47,420] [INFO] Task started: HMMsearch
[2024-01-25 19:40:47,420] [INFO] Running command: hmmsearch --tblout GCF_900292015.1_MB901379_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5e6b916-3cce-4d7c-a9b7-082bb9efd2ea/dqc_reference/reference_markers.hmm GCF_900292015.1_MB901379_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:47,671] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:47,672] [INFO] Found 6/6 markers.
[2024-01-25 19:40:47,717] [INFO] Query marker FASTA was written to GCF_900292015.1_MB901379_genomic.fna/markers.fasta
[2024-01-25 19:40:47,717] [INFO] Task started: Blastn
[2024-01-25 19:40:47,717] [INFO] Running command: blastn -query GCF_900292015.1_MB901379_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5e6b916-3cce-4d7c-a9b7-082bb9efd2ea/dqc_reference/reference_markers.fasta -out GCF_900292015.1_MB901379_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:48,657] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:48,660] [INFO] Selected 21 target genomes.
[2024-01-25 19:40:48,660] [INFO] Target genome list was writen to GCF_900292015.1_MB901379_genomic.fna/target_genomes.txt
[2024-01-25 19:40:48,669] [INFO] Task started: fastANI
[2024-01-25 19:40:48,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff4cd01-d12b-41c5-98cf-3308e44c4f19/GCF_900292015.1_MB901379_genomic.fna.gz --refList GCF_900292015.1_MB901379_genomic.fna/target_genomes.txt --output GCF_900292015.1_MB901379_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:41:19,943] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:19,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5e6b916-3cce-4d7c-a9b7-082bb9efd2ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:41:19,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5e6b916-3cce-4d7c-a9b7-082bb9efd2ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:41:19,956] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:41:19,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:41:19,956] [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 basiliense		GCA_900292015.1	2094119	2094119	type	True	100.0	1869	1869	95	conclusive
Mycobacterium pseudoshottsii	strain=JCM 15466	GCA_001515365.1	265949	265949	suspected-type	True	81.2904	1182	1869	95	below_threshold
Mycobacterium marinum	strain=CCUG20998	GCA_003391395.1	1781	1781	suspected-type	True	81.2193	1274	1869	95	below_threshold
Mycobacterium marinum	strain=DSM 44344	GCA_003431645.1	1781	1781	suspected-type	True	81.2118	1275	1869	95	below_threshold
Mycobacterium pseudoshottsii	strain=JCM 15466	GCA_003584745.1	265949	265949	suspected-type	True	81.1557	1252	1869	95	below_threshold
Mycobacterium gastri	strain=DSM 43505	GCA_002102175.1	1777	1777	type	True	80.9913	1150	1869	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	80.9749	1132	1869	95	below_threshold
Mycobacterium kansasii	strain=ATCC 12478	GCA_000157895.2	1768	1768	type	True	80.8599	1186	1869	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	80.8256	1183	1869	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	80.5093	1016	1869	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	80.4206	1058	1869	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	80.0883	911	1869	95	below_threshold
Mycobacterium tuberculosis variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	80.0228	889	1869	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	79.9447	964	1869	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	79.7678	947	1869	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	79.7601	901	1869	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	79.7125	844	1869	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	79.6927	851	1869	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	79.6628	838	1869	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	79.3978	859	1869	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	79.393	821	1869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:41:19,957] [INFO] DFAST Taxonomy check result was written to GCF_900292015.1_MB901379_genomic.fna/tc_result.tsv
[2024-01-25 19:41:19,958] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:41:19,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:41:19,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5e6b916-3cce-4d7c-a9b7-082bb9efd2ea/dqc_reference/checkm_data
[2024-01-25 19:41:19,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:41:20,011] [INFO] Task started: CheckM
[2024-01-25 19:41:20,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900292015.1_MB901379_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900292015.1_MB901379_genomic.fna/checkm_input GCF_900292015.1_MB901379_genomic.fna/checkm_result
[2024-01-25 19:43:08,865] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:08,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:08,888] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:08,888] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:08,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900292015.1_MB901379_genomic.fna/markers.fasta)
[2024-01-25 19:43:08,890] [INFO] Task started: Blastn
[2024-01-25 19:43:08,890] [INFO] Running command: blastn -query GCF_900292015.1_MB901379_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5e6b916-3cce-4d7c-a9b7-082bb9efd2ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_900292015.1_MB901379_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:10,255] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:10,257] [INFO] Selected 21 target genomes.
[2024-01-25 19:43:10,258] [INFO] Target genome list was writen to GCF_900292015.1_MB901379_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:10,276] [INFO] Task started: fastANI
[2024-01-25 19:43:10,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff4cd01-d12b-41c5-98cf-3308e44c4f19/GCF_900292015.1_MB901379_genomic.fna.gz --refList GCF_900292015.1_MB901379_genomic.fna/target_genomes_gtdb.txt --output GCF_900292015.1_MB901379_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:41,600] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:41,613] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:41,613] [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_900292015.1	s__Mycobacterium basiliense	100.0	1869	1869	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_003391395.1	s__Mycobacterium marinum	81.2344	1277	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.78	97.50	0.95	0.86	40	-
GCF_002102175.1	s__Mycobacterium gastri	80.9677	1154	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.95	99.95	0.95	0.95	2	-
GCF_900566055.1	s__Mycobacterium innocens	80.9538	1135	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_000157895.3	s__Mycobacterium kansasii	80.8702	1184	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.15	0.98	0.95	35	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	80.8308	1180	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_002086675.1	s__Mycobacterium persicum	80.728	1133	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_010731535.1	s__Mycobacterium lacus	80.4221	1058	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002104675.1	s__Mycobacterium decipiens	80.3132	1008	1869	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	80.0759	913	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
GCF_002086155.1	s__Mycobacterium angelicum	80.0319	1044	1869	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	79.9021	969	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001954275.1	s__Mycobacterium sp001954275	79.8197	890	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_001668725.1	s__Mycobacterium sp001668725	79.7958	927	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_002116635.1	s__Mycobacterium szulgai	79.7877	1060	1869	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	79.6658	931	1869	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	79.6626	972	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689175.1	s__Mycobacterium kubicae	79.6517	859	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCA_004298145.1	s__Mycobacterium sp004298145	79.4525	832	1869	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	79.3889	821	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_000613245.1	s__Mycobacterium asiaticum	79.2691	872	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.95	98.52	0.95	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:41,614] [INFO] GTDB search result was written to GCF_900292015.1_MB901379_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:41,615] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:41,618] [INFO] DFAST_QC result json was written to GCF_900292015.1_MB901379_genomic.fna/dqc_result.json
[2024-01-25 19:43:41,618] [INFO] DFAST_QC completed!
[2024-01-25 19:43:41,618] [INFO] Total running time: 0h3m36s