[2024-01-24 11:44:38,166] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f3a1e07-68c5-41ec-bb40-5b3e20783b1d/dqc_reference
[2024-01-24 11:44:41,489] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,490] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,490] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5891418-d639-4366-a677-7b9cd08c66cd/GCF_002355775.1_ASM235577v1_genomic.fna.gz | prodigal -d GCF_002355775.1_ASM235577v1_genomic.fna/cds.fna -a GCF_002355775.1_ASM235577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:45:14,260] [INFO] Task succeeded: Prodigal
[2024-01-24 11:45:14,260] [INFO] Task started: HMMsearch
[2024-01-24 11:45:14,260] [INFO] Running command: hmmsearch --tblout GCF_002355775.1_ASM235577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f3a1e07-68c5-41ec-bb40-5b3e20783b1d/dqc_reference/reference_markers.hmm GCF_002355775.1_ASM235577v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:45:14,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:45:14,541] [INFO] Found 6/6 markers.
[2024-01-24 11:45:14,591] [INFO] Query marker FASTA was written to GCF_002355775.1_ASM235577v1_genomic.fna/markers.fasta
[2024-01-24 11:45:14,592] [INFO] Task started: Blastn
[2024-01-24 11:45:14,592] [INFO] Running command: blastn -query GCF_002355775.1_ASM235577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f3a1e07-68c5-41ec-bb40-5b3e20783b1d/dqc_reference/reference_markers.fasta -out GCF_002355775.1_ASM235577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:15,656] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:15,659] [INFO] Selected 6 target genomes.
[2024-01-24 11:45:15,660] [INFO] Target genome list was writen to GCF_002355775.1_ASM235577v1_genomic.fna/target_genomes.txt
[2024-01-24 11:45:15,663] [INFO] Task started: fastANI
[2024-01-24 11:45:15,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5891418-d639-4366-a677-7b9cd08c66cd/GCF_002355775.1_ASM235577v1_genomic.fna.gz --refList GCF_002355775.1_ASM235577v1_genomic.fna/target_genomes.txt --output GCF_002355775.1_ASM235577v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:43,337] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:43,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f3a1e07-68c5-41ec-bb40-5b3e20783b1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:43,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f3a1e07-68c5-41ec-bb40-5b3e20783b1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:43,352] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 11:45:43,352] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:45:43,352] [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 pseudoshottsii	strain=JCM 15466	GCA_003584745.1	265949	265949	suspected-type	True	99.1083	1827	2021	95	inconclusive
Mycobacterium pseudoshottsii	strain=JCM 15466	GCA_001515365.1	265949	265949	suspected-type	True	99.079	1758	2021	95	inconclusive
Mycobacterium marinum	strain=CCUG20998	GCA_003391395.1	1781	1781	suspected-type	True	97.8543	1827	2021	95	inconclusive
Mycobacterium marinum	strain=DSM 44344	GCA_003431645.1	1781	1781	suspected-type	True	97.8327	1800	2021	95	inconclusive
Mycobacterium marinum	strain=NCTC2275	GCA_003431655.1	1781	1781	suspected-type	True	97.7903	1801	2021	95	inconclusive
Mycobacterium shottsii	strain=JCM 12657	GCA_010728525.1	133549	133549	suspected-type	True	97.2529	1706	2021	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 11:45:43,354] [INFO] DFAST Taxonomy check result was written to GCF_002355775.1_ASM235577v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:43,355] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:43,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:43,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f3a1e07-68c5-41ec-bb40-5b3e20783b1d/dqc_reference/checkm_data
[2024-01-24 11:45:43,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:43,436] [INFO] Task started: CheckM
[2024-01-24 11:45:43,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002355775.1_ASM235577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002355775.1_ASM235577v1_genomic.fna/checkm_input GCF_002355775.1_ASM235577v1_genomic.fna/checkm_result
[2024-01-24 11:47:06,354] [INFO] Task succeeded: CheckM
[2024-01-24 11:47:06,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:47:06,381] [INFO] ===== Completeness check finished =====
[2024-01-24 11:47:06,381] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:47:06,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002355775.1_ASM235577v1_genomic.fna/markers.fasta)
[2024-01-24 11:47:06,382] [INFO] Task started: Blastn
[2024-01-24 11:47:06,382] [INFO] Running command: blastn -query GCF_002355775.1_ASM235577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f3a1e07-68c5-41ec-bb40-5b3e20783b1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002355775.1_ASM235577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:47:07,852] [INFO] Task succeeded: Blastn
[2024-01-24 11:47:07,857] [INFO] Selected 17 target genomes.
[2024-01-24 11:47:07,857] [INFO] Target genome list was writen to GCF_002355775.1_ASM235577v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:47:07,870] [INFO] Task started: fastANI
[2024-01-24 11:47:07,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5891418-d639-4366-a677-7b9cd08c66cd/GCF_002355775.1_ASM235577v1_genomic.fna.gz --refList GCF_002355775.1_ASM235577v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002355775.1_ASM235577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:47:33,148] [INFO] Task succeeded: fastANI
[2024-01-24 11:47:33,162] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:47:33,162] [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_003391395.1	s__Mycobacterium marinum	97.8415	1828	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.78	97.50	0.95	0.86	40	conclusive
GCF_900292015.1	s__Mycobacterium basiliense	81.0266	1218	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566055.1	s__Mycobacterium innocens	80.9945	1120	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002705925.1	s__Mycobacterium ostraviense	80.8674	1189	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	80.7789	1177	2021	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	80.7338	1102	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_009741445.1	s__Mycobacterium avium	80.36	901	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCF_002086155.1	s__Mycobacterium angelicum	80.2387	1077	2021	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	80.1852	967	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002116635.1	s__Mycobacterium szulgai	80.0158	1059	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614435.1	s__Mycobacterium paragordonae	79.9698	1004	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_001417955.2	s__Mycobacterium gordonae_B	79.9009	972	2021	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	79.845	880	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCF_002101675.1	s__Mycobacterium gordonae	79.6773	998	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	-
GCF_010729105.1	s__Mycobacterium saskatchewanense	79.6391	866	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_017086405.1	s__Mycobacterium gordonae_D	79.6218	990	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112775.1	s__Mycobacterium montefiorense	79.3354	872	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:47:33,164] [INFO] GTDB search result was written to GCF_002355775.1_ASM235577v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:47:33,164] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:47:33,169] [INFO] DFAST_QC result json was written to GCF_002355775.1_ASM235577v1_genomic.fna/dqc_result.json
[2024-01-24 11:47:33,169] [INFO] DFAST_QC completed!
[2024-01-24 11:47:33,169] [INFO] Total running time: 0h2m55s