[2024-01-24 11:59:13,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:13,006] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:13,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg5af64e0c-d8d4-4352-8932-ab3471cb2716/dqc_reference
[2024-01-24 11:59:14,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,528] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,528] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb4f70e8-7206-4ad3-8f7e-3c0cb6f76344/GCF_025822425.1_ASM2582242v1_genomic.fna.gz | prodigal -d GCF_025822425.1_ASM2582242v1_genomic.fna/cds.fna -a GCF_025822425.1_ASM2582242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:41,682] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:41,682] [INFO] Task started: HMMsearch
[2024-01-24 11:59:41,683] [INFO] Running command: hmmsearch --tblout GCF_025822425.1_ASM2582242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5af64e0c-d8d4-4352-8932-ab3471cb2716/dqc_reference/reference_markers.hmm GCF_025822425.1_ASM2582242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:42,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:42,089] [INFO] Found 6/6 markers.
[2024-01-24 11:59:42,157] [INFO] Query marker FASTA was written to GCF_025822425.1_ASM2582242v1_genomic.fna/markers.fasta
[2024-01-24 11:59:42,157] [INFO] Task started: Blastn
[2024-01-24 11:59:42,157] [INFO] Running command: blastn -query GCF_025822425.1_ASM2582242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af64e0c-d8d4-4352-8932-ab3471cb2716/dqc_reference/reference_markers.fasta -out GCF_025822425.1_ASM2582242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:43,417] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:43,420] [INFO] Selected 14 target genomes.
[2024-01-24 11:59:43,421] [INFO] Target genome list was writen to GCF_025822425.1_ASM2582242v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:43,426] [INFO] Task started: fastANI
[2024-01-24 11:59:43,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb4f70e8-7206-4ad3-8f7e-3c0cb6f76344/GCF_025822425.1_ASM2582242v1_genomic.fna.gz --refList GCF_025822425.1_ASM2582242v1_genomic.fna/target_genomes.txt --output GCF_025822425.1_ASM2582242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:05,649] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:05,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5af64e0c-d8d4-4352-8932-ab3471cb2716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:05,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5af64e0c-d8d4-4352-8932-ab3471cb2716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:05,667] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:05,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:05,667] [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 peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	99.9847	2289	2328	95	conclusive
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	88.2519	1784	2328	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	88.2208	1796	2328	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	87.9843	1756	2328	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	87.9473	1751	2328	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	87.9286	1789	2328	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	87.8478	1567	2328	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	87.8472	1828	2328	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	87.7582	1616	2328	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	87.0035	1706	2328	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.4217	891	2328	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.3496	898	2328	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.3346	853	2328	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.0195	865	2328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:05,669] [INFO] DFAST Taxonomy check result was written to GCF_025822425.1_ASM2582242v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:05,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:05,670] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:05,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5af64e0c-d8d4-4352-8932-ab3471cb2716/dqc_reference/checkm_data
[2024-01-24 12:00:05,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:05,736] [INFO] Task started: CheckM
[2024-01-24 12:00:05,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822425.1_ASM2582242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822425.1_ASM2582242v1_genomic.fna/checkm_input GCF_025822425.1_ASM2582242v1_genomic.fna/checkm_result
[2024-01-24 12:01:19,288] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:19,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:19,315] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:19,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:19,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822425.1_ASM2582242v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:19,316] [INFO] Task started: Blastn
[2024-01-24 12:01:19,316] [INFO] Running command: blastn -query GCF_025822425.1_ASM2582242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af64e0c-d8d4-4352-8932-ab3471cb2716/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822425.1_ASM2582242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:21,031] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:21,035] [INFO] Selected 10 target genomes.
[2024-01-24 12:01:21,035] [INFO] Target genome list was writen to GCF_025822425.1_ASM2582242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:21,043] [INFO] Task started: fastANI
[2024-01-24 12:01:21,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb4f70e8-7206-4ad3-8f7e-3c0cb6f76344/GCF_025822425.1_ASM2582242v1_genomic.fna.gz --refList GCF_025822425.1_ASM2582242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822425.1_ASM2582242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:37,545] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:37,563] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:37,564] [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_002102345.1	s__Mycobacterium peregrinum	99.9847	2289	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	98.27	0.94	0.91	5	conclusive
GCF_001665625.1	s__Mycobacterium peregrinum_B	94.2369	1836	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.32	98.32	0.89	0.89	2	-
GCF_001665785.1	s__Mycobacterium peregrinum_A	93.8456	1882	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011745145.1	s__Mycobacterium sp011745145	89.0162	1774	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455325.1	s__Mycobacterium septicum	88.2134	1797	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_000295855.1	s__Mycobacterium fortuitum	87.949	1751	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_010727325.1	s__Mycobacterium alvei	87.843	1567	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876775.1	s__Mycobacterium lutetiense	87.7451	1618	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004762045.1	s__Mycobacterium sp004762045	87.644	1727	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942625.1	s__Mycobacterium syngnathidarum	86.6232	1647	2328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:37,566] [INFO] GTDB search result was written to GCF_025822425.1_ASM2582242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:37,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:37,572] [INFO] DFAST_QC result json was written to GCF_025822425.1_ASM2582242v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:37,572] [INFO] DFAST_QC completed!
[2024-01-24 12:01:37,572] [INFO] Total running time: 0h2m25s