[2024-01-24 14:11:46,657] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg7badcf67-d51c-458c-9295-ccf967731d1c/dqc_reference
[2024-01-24 14:11:48,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:48,879] [INFO] Task started: Prodigal
[2024-01-24 14:11:48,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg75a1212d-2218-4c56-8ffb-01651385bfd2/GCF_002101665.1_ASM210166v1_genomic.fna.gz | prodigal -d GCF_002101665.1_ASM210166v1_genomic.fna/cds.fna -a GCF_002101665.1_ASM210166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:11,612] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:11,612] [INFO] Task started: HMMsearch
[2024-01-24 14:12:11,612] [INFO] Running command: hmmsearch --tblout GCF_002101665.1_ASM210166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7badcf67-d51c-458c-9295-ccf967731d1c/dqc_reference/reference_markers.hmm GCF_002101665.1_ASM210166v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:11,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:11,992] [INFO] Found 6/6 markers.
[2024-01-24 14:12:12,044] [INFO] Query marker FASTA was written to GCF_002101665.1_ASM210166v1_genomic.fna/markers.fasta
[2024-01-24 14:12:12,045] [INFO] Task started: Blastn
[2024-01-24 14:12:12,045] [INFO] Running command: blastn -query GCF_002101665.1_ASM210166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7badcf67-d51c-458c-9295-ccf967731d1c/dqc_reference/reference_markers.fasta -out GCF_002101665.1_ASM210166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:13,447] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:13,450] [INFO] Selected 10 target genomes.
[2024-01-24 14:12:13,451] [INFO] Target genome list was writen to GCF_002101665.1_ASM210166v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:13,461] [INFO] Task started: fastANI
[2024-01-24 14:12:13,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg75a1212d-2218-4c56-8ffb-01651385bfd2/GCF_002101665.1_ASM210166v1_genomic.fna.gz --refList GCF_002101665.1_ASM210166v1_genomic.fna/target_genomes.txt --output GCF_002101665.1_ASM210166v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:26,611] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:26,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7badcf67-d51c-458c-9295-ccf967731d1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:26,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7badcf67-d51c-458c-9295-ccf967731d1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:26,624] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:12:26,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:26,624] [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
Mycobacteroides immunogenum	strain=ATCC 700505	GCA_002101665.1	83262	83262	type	True	100.0	1827	1830	95	conclusive
Mycobacteroides immunogenum	strain=MC 779	GCA_002013555.1	83262	83262	type	True	99.9979	1815	1830	95	conclusive
Mycobacteroides immunogenum	strain=CCUG 47286	GCA_001605725.1	83262	83262	type	True	99.9918	1829	1830	95	conclusive
Mycobacteroides franklinii	strain=DSM 45524	GCA_002086225.1	948102	948102	type	True	86.5291	1401	1830	95	below_threshold
Mycobacteroides abscessus subsp. massiliense	strain=JCM 15300	GCA_000497265.2	1962118	36809	type	True	86.4588	1335	1830	95	below_threshold
Mycobacteroides abscessus subsp. massiliense	strain=CCUG 48898	GCA_000239055.2	1962118	36809	type	True	86.3881	1315	1830	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=BD	GCA_000239035.2	319705	36809	type	True	86.3743	1347	1830	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=CCUG 50184	GCA_006409125.1	319705	36809	type	True	86.3459	1336	1830	95	below_threshold
Mycobacteroides saopaulense	strain=CCUG 66554	GCA_002086715.1	1578165	1578165	type	True	85.3692	1269	1830	95	below_threshold
Mycobacteroides saopaulense	strain=EPM10906	GCA_001456355.1	1578165	1578165	type	True	85.047	1297	1830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:26,626] [INFO] DFAST Taxonomy check result was written to GCF_002101665.1_ASM210166v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:26,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:26,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:26,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7badcf67-d51c-458c-9295-ccf967731d1c/dqc_reference/checkm_data
[2024-01-24 14:12:26,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:26,693] [INFO] Task started: CheckM
[2024-01-24 14:12:26,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101665.1_ASM210166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101665.1_ASM210166v1_genomic.fna/checkm_input GCF_002101665.1_ASM210166v1_genomic.fna/checkm_result
[2024-01-24 14:13:31,421] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:31,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:31,445] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:31,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:31,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101665.1_ASM210166v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:31,446] [INFO] Task started: Blastn
[2024-01-24 14:13:31,446] [INFO] Running command: blastn -query GCF_002101665.1_ASM210166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7badcf67-d51c-458c-9295-ccf967731d1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101665.1_ASM210166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:36,899] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:36,904] [INFO] Selected 9 target genomes.
[2024-01-24 14:13:36,904] [INFO] Target genome list was writen to GCF_002101665.1_ASM210166v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:36,913] [INFO] Task started: fastANI
[2024-01-24 14:13:36,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg75a1212d-2218-4c56-8ffb-01651385bfd2/GCF_002101665.1_ASM210166v1_genomic.fna.gz --refList GCF_002101665.1_ASM210166v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101665.1_ASM210166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:49,069] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:49,130] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:49,131] [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_001605725.1	s__Mycobacterium immunogenum	99.9918	1829	1830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	96.59	0.98	0.90	18	conclusive
GCF_002013895.1	s__Mycobacterium franklinii	86.5563	1415	1830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.20	95.66	0.94	0.87	12	-
GCA_000069185.1	s__Mycobacterium abscessus	86.4197	1366	1830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	96.83	0.93	0.86	1820	-
GCF_001456355.1	s__Mycobacterium saopaulense	85.047	1297	1830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.82	98.51	0.95	0.95	4	-
GCF_014204435.1	s__Mycobacterium chelonae_A	84.5863	1084	1830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004924335.1	s__Mycobacterium salmoniphilum	84.1756	1271	1830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.49	96.58	0.95	0.92	5	-
GCF_002356335.1	s__Mycobacterium stephanolepidis	84.1488	1272	1830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013465.1	s__Mycobacterium sp002013465	84.1327	1249	1830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.45	95.17	0.93	0.91	7	-
GCF_002013415.1	s__Mycobacterium sp002013415	84.0689	1256	1830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.14	98.85	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:49,132] [INFO] GTDB search result was written to GCF_002101665.1_ASM210166v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:49,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:49,136] [INFO] DFAST_QC result json was written to GCF_002101665.1_ASM210166v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:49,136] [INFO] DFAST_QC completed!
[2024-01-24 14:13:49,136] [INFO] Total running time: 0h2m2s