[2024-01-24 13:01:12,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg0632f0cd-19ba-4177-b8c1-2607d4bf86c2/dqc_reference
[2024-01-24 13:01:13,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,718] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,718] [INFO] Running command: gunzip -c /var/lib/cwl/stgf84ac349-54eb-4893-88f6-05094380b5b9/GCF_002102025.1_ASM210202v1_genomic.fna.gz | prodigal -d GCF_002102025.1_ASM210202v1_genomic.fna/cds.fna -a GCF_002102025.1_ASM210202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:30,427] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:30,427] [INFO] Task started: HMMsearch
[2024-01-24 13:01:30,427] [INFO] Running command: hmmsearch --tblout GCF_002102025.1_ASM210202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0632f0cd-19ba-4177-b8c1-2607d4bf86c2/dqc_reference/reference_markers.hmm GCF_002102025.1_ASM210202v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:30,738] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:30,739] [INFO] Found 6/6 markers.
[2024-01-24 13:01:30,784] [INFO] Query marker FASTA was written to GCF_002102025.1_ASM210202v1_genomic.fna/markers.fasta
[2024-01-24 13:01:30,785] [INFO] Task started: Blastn
[2024-01-24 13:01:30,785] [INFO] Running command: blastn -query GCF_002102025.1_ASM210202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0632f0cd-19ba-4177-b8c1-2607d4bf86c2/dqc_reference/reference_markers.fasta -out GCF_002102025.1_ASM210202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:31,933] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:31,937] [INFO] Selected 17 target genomes.
[2024-01-24 13:01:31,937] [INFO] Target genome list was writen to GCF_002102025.1_ASM210202v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:31,943] [INFO] Task started: fastANI
[2024-01-24 13:01:31,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84ac349-54eb-4893-88f6-05094380b5b9/GCF_002102025.1_ASM210202v1_genomic.fna.gz --refList GCF_002102025.1_ASM210202v1_genomic.fna/target_genomes.txt --output GCF_002102025.1_ASM210202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:53,536] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:53,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0632f0cd-19ba-4177-b8c1-2607d4bf86c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:53,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0632f0cd-19ba-4177-b8c1-2607d4bf86c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:53,550] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:53,550] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:53,551] [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_002102025.1	56425	56425	type	True	100.0	1761	1780	95	conclusive
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	99.7771	1660	1780	95	conclusive
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	84.1573	1187	1780	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	84.1239	1330	1780	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	84.123	1163	1780	95	below_threshold
Mycobacterium saskatchewanense	strain=DSM 44616	GCA_002101875.1	220927	220927	type	True	84.0144	1255	1780	95	below_threshold
Mycobacterium saskatchewanense	strain=JCM 13016	GCA_010729105.1	220927	220927	type	True	83.9979	1299	1780	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	83.7018	1217	1780	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	83.6498	1189	1780	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	83.6456	1282	1780	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	83.6226	1103	1780	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	83.3114	1241	1780	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	83.2862	1293	1780	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	83.1732	1180	1780	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	83.1568	1188	1780	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	81.6927	1169	1780	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	80.7293	1009	1780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:53,553] [INFO] DFAST Taxonomy check result was written to GCF_002102025.1_ASM210202v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:53,554] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:53,554] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:53,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0632f0cd-19ba-4177-b8c1-2607d4bf86c2/dqc_reference/checkm_data
[2024-01-24 13:01:53,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:53,606] [INFO] Task started: CheckM
[2024-01-24 13:01:53,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002102025.1_ASM210202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002102025.1_ASM210202v1_genomic.fna/checkm_input GCF_002102025.1_ASM210202v1_genomic.fna/checkm_result
[2024-01-24 13:02:46,048] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:46,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:46,067] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:46,067] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:46,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002102025.1_ASM210202v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:46,068] [INFO] Task started: Blastn
[2024-01-24 13:02:46,068] [INFO] Running command: blastn -query GCF_002102025.1_ASM210202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0632f0cd-19ba-4177-b8c1-2607d4bf86c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002102025.1_ASM210202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:47,656] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:47,660] [INFO] Selected 18 target genomes.
[2024-01-24 13:02:47,661] [INFO] Target genome list was writen to GCF_002102025.1_ASM210202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:47,671] [INFO] Task started: fastANI
[2024-01-24 13:02:47,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84ac349-54eb-4893-88f6-05094380b5b9/GCF_002102025.1_ASM210202v1_genomic.fna.gz --refList GCF_002102025.1_ASM210202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002102025.1_ASM210202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:11,277] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:11,291] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:11,291] [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	99.7771	1660	1780	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	84.5773	1333	1780	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	84.1324	1328	1780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_900078675.2	s__Mycobacterium interjectum	84.0284	1337	1780	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	84.0208	1296	1780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001668725.1	s__Mycobacterium sp001668725	83.9894	1347	1780	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	83.9682	1347	1780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	83.9033	1290	1780	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	83.8861	1289	1780	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	83.7847	1389	1780	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	83.7061	1277	1780	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	83.6766	1220	1780	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	83.6741	1244	1780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_001672815.1	s__Mycobacterium sp001672815	83.6054	1252	1780	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	83.5964	1272	1780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.16	95.96	0.85	0.84	3	-
GCF_001665605.1	s__Mycobacterium sp001665605	83.2987	1258	1780	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	83.1934	1245	1780	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	82.9531	1197	1780	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 13:03:11,293] [INFO] GTDB search result was written to GCF_002102025.1_ASM210202v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:11,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:11,297] [INFO] DFAST_QC result json was written to GCF_002102025.1_ASM210202v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:11,297] [INFO] DFAST_QC completed!
[2024-01-24 13:03:11,298] [INFO] Total running time: 0h1m59s