[2023-07-01 06:50:34,330] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:50:34,332] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:50:34,332] [INFO] DQC Reference Directory: /var/lib/cwl/stga581bd45-80f6-4a3d-b062-ea36b603296c/dqc_reference
[2023-07-01 06:50:35,527] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:50:35,528] [INFO] Task started: Prodigal
[2023-07-01 06:50:35,528] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5d37d75-1f9e-4f32-a09b-4a75cb759b76/GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna.gz | prodigal -d GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/cds.fna -a GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:50:52,789] [INFO] Task succeeded: Prodigal
[2023-07-01 06:50:52,790] [INFO] Task started: HMMsearch
[2023-07-01 06:50:52,790] [INFO] Running command: hmmsearch --tblout GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga581bd45-80f6-4a3d-b062-ea36b603296c/dqc_reference/reference_markers.hmm GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:50:53,055] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:50:53,056] [INFO] Found 6/6 markers.
[2023-07-01 06:50:53,106] [INFO] Query marker FASTA was written to GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/markers.fasta
[2023-07-01 06:50:53,107] [INFO] Task started: Blastn
[2023-07-01 06:50:53,107] [INFO] Running command: blastn -query GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga581bd45-80f6-4a3d-b062-ea36b603296c/dqc_reference/reference_markers.fasta -out GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:50:54,303] [INFO] Task succeeded: Blastn
[2023-07-01 06:50:54,307] [INFO] Selected 14 target genomes.
[2023-07-01 06:50:54,307] [INFO] Target genome list was writen to GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/target_genomes.txt
[2023-07-01 06:50:54,309] [INFO] Task started: fastANI
[2023-07-01 06:50:54,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5d37d75-1f9e-4f32-a09b-4a75cb759b76/GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna.gz --refList GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/target_genomes.txt --output GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:51:11,337] [INFO] Task succeeded: fastANI
[2023-07-01 06:51:11,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga581bd45-80f6-4a3d-b062-ea36b603296c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:51:11,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga581bd45-80f6-4a3d-b062-ea36b603296c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:51:11,349] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:51:11,349] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 06:51:11,350] [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
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	84.5121	1398	1876	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	84.4983	1391	1876	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	84.3465	1328	1876	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	84.3296	1341	1876	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	84.2305	1369	1876	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	84.1713	1261	1876	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	81.0157	1118	1876	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	81.0123	1118	1876	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	79.9564	875	1876	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.7088	811	1876	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6797	827	1876	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.6057	819	1876	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.6029	823	1876	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.4687	812	1876	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 06:51:11,352] [INFO] DFAST Taxonomy check result was written to GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/tc_result.tsv
[2023-07-01 06:51:11,352] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:51:11,352] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:51:11,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga581bd45-80f6-4a3d-b062-ea36b603296c/dqc_reference/checkm_data
[2023-07-01 06:51:11,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:51:11,405] [INFO] Task started: CheckM
[2023-07-01 06:51:11,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/checkm_input GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/checkm_result
[2023-07-01 06:52:08,000] [INFO] Task succeeded: CheckM
[2023-07-01 06:52:08,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 06:52:08,019] [INFO] ===== Completeness check finished =====
[2023-07-01 06:52:08,019] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:52:08,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/markers.fasta)
[2023-07-01 06:52:08,020] [INFO] Task started: Blastn
[2023-07-01 06:52:08,020] [INFO] Running command: blastn -query GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga581bd45-80f6-4a3d-b062-ea36b603296c/dqc_reference/reference_markers_gtdb.fasta -out GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:52:09,745] [INFO] Task succeeded: Blastn
[2023-07-01 06:52:09,749] [INFO] Selected 13 target genomes.
[2023-07-01 06:52:09,749] [INFO] Target genome list was writen to GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:52:09,753] [INFO] Task started: fastANI
[2023-07-01 06:52:09,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5d37d75-1f9e-4f32-a09b-4a75cb759b76/GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna.gz --refList GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:52:28,918] [INFO] Task succeeded: fastANI
[2023-07-01 06:52:28,929] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 06:52:28,930] [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_001044245.1	s__Mycobacterium obuense	98.256	1674	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	conclusive
GCF_007096635.1	s__Mycobacterium sp007096635	87.1605	1461	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000762985.1	s__Mycobacterium rufum_A	84.8843	1410	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	84.5013	1391	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_001044255.1	s__Mycobacterium chubuense	84.3552	1326	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	84.156	1263	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
GCF_001545925.1	s__Mycobacterium sp001545925	82.1956	889	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190915.1	s__Mycobacterium iranicum_B	81.4972	1073	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637195.1	s__Mycobacterium aurum	81.0375	1113	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002086115.1	s__Mycobacterium bacteremicum	79.9556	876	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001494595.1	s__Mycobacterium sp001494595	79.7912	853	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731855.1	s__Mycobacterium anyangense	79.6027	822	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362315.1	s__Mycobacterium sp004362315	79.5594	852	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
--------------------------------------------------------------------------------
[2023-07-01 06:52:28,931] [INFO] GTDB search result was written to GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/result_gtdb.tsv
[2023-07-01 06:52:28,932] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:52:28,953] [INFO] DFAST_QC result json was written to GCA_943913265.1_u2DneDdYfL_bin.5.MAG_genomic.fna/dqc_result.json
[2023-07-01 06:52:28,953] [INFO] DFAST_QC completed!
[2023-07-01 06:52:28,953] [INFO] Total running time: 0h1m55s