[2024-01-24 15:26:55,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,046] [INFO] DQC Reference Directory: /var/lib/cwl/stge2924bc7-bb34-4f4a-87c2-215c2e4ae514/dqc_reference
[2024-01-24 15:26:56,277] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,278] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,279] [INFO] Running command: gunzip -c /var/lib/cwl/stgddc88a7b-ef30-436e-a6d5-79c26380e5bb/GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna.gz | prodigal -d GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/cds.fna -a GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:12,878] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:12,879] [INFO] Task started: HMMsearch
[2024-01-24 15:27:12,879] [INFO] Running command: hmmsearch --tblout GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2924bc7-bb34-4f4a-87c2-215c2e4ae514/dqc_reference/reference_markers.hmm GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:13,178] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:13,179] [INFO] Found 6/6 markers.
[2024-01-24 15:27:13,228] [INFO] Query marker FASTA was written to GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/markers.fasta
[2024-01-24 15:27:13,228] [INFO] Task started: Blastn
[2024-01-24 15:27:13,228] [INFO] Running command: blastn -query GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2924bc7-bb34-4f4a-87c2-215c2e4ae514/dqc_reference/reference_markers.fasta -out GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:14,409] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:14,413] [INFO] Selected 17 target genomes.
[2024-01-24 15:27:14,413] [INFO] Target genome list was writen to GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:14,421] [INFO] Task started: fastANI
[2024-01-24 15:27:14,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgddc88a7b-ef30-436e-a6d5-79c26380e5bb/GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna.gz --refList GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/target_genomes.txt --output GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:37,361] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:37,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2924bc7-bb34-4f4a-87c2-215c2e4ae514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:37,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2924bc7-bb34-4f4a-87c2-215c2e4ae514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:37,375] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:37,375] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:37,375] [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 bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	99.9995	1689	1691	95	conclusive
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	99.8095	1644	1691	95	conclusive
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	84.0787	1108	1691	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	84.0669	1126	1691	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	84.0451	1289	1691	95	below_threshold
Mycobacterium saskatchewanense	strain=JCM 13016	GCA_010729105.1	220927	220927	type	True	83.9557	1236	1691	95	below_threshold
Mycobacterium saskatchewanense	strain=DSM 44616	GCA_002101875.1	220927	220927	type	True	83.9245	1220	1691	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	83.6516	1074	1691	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	83.6366	1157	1691	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	83.5256	1143	1691	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	83.5146	1231	1691	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	83.2574	1206	1691	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	83.2114	1231	1691	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	83.1048	1133	1691	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	83.0778	1134	1691	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	81.6955	1087	1691	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	80.6364	968	1691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:37,377] [INFO] DFAST Taxonomy check result was written to GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:37,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:37,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:37,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2924bc7-bb34-4f4a-87c2-215c2e4ae514/dqc_reference/checkm_data
[2024-01-24 15:27:37,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:37,426] [INFO] Task started: CheckM
[2024-01-24 15:27:37,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/checkm_input GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/checkm_result
[2024-01-24 15:28:25,174] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:25,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:25,191] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:25,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:25,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/markers.fasta)
[2024-01-24 15:28:25,192] [INFO] Task started: Blastn
[2024-01-24 15:28:25,192] [INFO] Running command: blastn -query GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2924bc7-bb34-4f4a-87c2-215c2e4ae514/dqc_reference/reference_markers_gtdb.fasta -out GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:26,829] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:26,832] [INFO] Selected 18 target genomes.
[2024-01-24 15:28:26,832] [INFO] Target genome list was writen to GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:26,860] [INFO] Task started: fastANI
[2024-01-24 15:28:26,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgddc88a7b-ef30-436e-a6d5-79c26380e5bb/GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna.gz --refList GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/target_genomes_gtdb.txt --output GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:51,459] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:51,473] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:51,473] [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_001053185.1	s__Mycobacterium bohemicum	99.9995	1689	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	conclusive
GCF_902652685.1	s__Mycobacterium sp902652685	84.4094	1269	1691	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	84.0443	1297	1691	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	84.0436	1289	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001668725.1	s__Mycobacterium sp001668725	83.9876	1284	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCA_002102225.1	s__Mycobacterium interjectum_B	83.9518	1289	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729105.1	s__Mycobacterium saskatchewanense	83.928	1240	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001673535.1	s__Mycobacterium sp001673535	83.8674	1236	1691	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	83.8334	1302	1691	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	83.7185	1260	1691	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	83.6494	1226	1691	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	83.648	1155	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455205.1	s__Mycobacterium sp000455205	83.6127	1199	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.16	95.96	0.85	0.84	3	-
GCF_001672815.1	s__Mycobacterium sp001672815	83.5724	1198	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	83.4887	1184	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_001665605.1	s__Mycobacterium sp001665605	83.2645	1198	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.77	98.77	0.96	0.96	2	-
GCF_001667075.1	s__Mycobacterium sp001667075	83.0683	1199	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.38	0.97	0.97	3	-
GCF_001953985.1	s__Mycobacterium colombiense_B	82.931	1140	1691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:51,475] [INFO] GTDB search result was written to GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:51,475] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:51,479] [INFO] DFAST_QC result json was written to GCF_001053185.1_PRJEB5741_assembly_1_genomic.fna/dqc_result.json
[2024-01-24 15:28:51,479] [INFO] DFAST_QC completed!
[2024-01-24 15:28:51,479] [INFO] Total running time: 0h1m56s