[2024-01-24 13:57:57,478] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:57,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:57,480] [INFO] DQC Reference Directory: /var/lib/cwl/stga7c9e11b-68d2-49a7-8e87-4f3b16cc1306/dqc_reference
[2024-01-24 13:57:58,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:58,783] [INFO] Task started: Prodigal
[2024-01-24 13:57:58,783] [INFO] Running command: gunzip -c /var/lib/cwl/stg92ee4137-8092-4646-914c-9c7431c66f2f/GCF_003855255.1_ASM385525v1_genomic.fna.gz | prodigal -d GCF_003855255.1_ASM385525v1_genomic.fna/cds.fna -a GCF_003855255.1_ASM385525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:31,683] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:31,684] [INFO] Task started: HMMsearch
[2024-01-24 13:58:31,684] [INFO] Running command: hmmsearch --tblout GCF_003855255.1_ASM385525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7c9e11b-68d2-49a7-8e87-4f3b16cc1306/dqc_reference/reference_markers.hmm GCF_003855255.1_ASM385525v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:32,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:32,058] [INFO] Found 6/6 markers.
[2024-01-24 13:58:32,117] [INFO] Query marker FASTA was written to GCF_003855255.1_ASM385525v1_genomic.fna/markers.fasta
[2024-01-24 13:58:32,118] [INFO] Task started: Blastn
[2024-01-24 13:58:32,118] [INFO] Running command: blastn -query GCF_003855255.1_ASM385525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7c9e11b-68d2-49a7-8e87-4f3b16cc1306/dqc_reference/reference_markers.fasta -out GCF_003855255.1_ASM385525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:33,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:33,382] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:33,382] [INFO] Target genome list was writen to GCF_003855255.1_ASM385525v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:33,473] [INFO] Task started: fastANI
[2024-01-24 13:58:33,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg92ee4137-8092-4646-914c-9c7431c66f2f/GCF_003855255.1_ASM385525v1_genomic.fna.gz --refList GCF_003855255.1_ASM385525v1_genomic.fna/target_genomes.txt --output GCF_003855255.1_ASM385525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:58,090] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:58,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7c9e11b-68d2-49a7-8e87-4f3b16cc1306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:58,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7c9e11b-68d2-49a7-8e87-4f3b16cc1306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:58,103] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:58,103] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:58,103] [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 nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	100.0	2301	2301	95	inconclusive
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	95.1654	1904	2301	95	inconclusive
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	95.1544	1928	2301	95	inconclusive
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	89.1538	1820	2301	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	88.8119	1799	2301	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	88.0877	1726	2301	95	below_threshold
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	87.8279	1799	2301	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	87.5296	1521	2301	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	87.4642	1584	2301	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	86.8441	1699	2301	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	86.738	1725	2301	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.1835	953	2301	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.6593	909	2301	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6331	901	2301	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.2472	921	2301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:58,104] [INFO] DFAST Taxonomy check result was written to GCF_003855255.1_ASM385525v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:58,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:58,105] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:58,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7c9e11b-68d2-49a7-8e87-4f3b16cc1306/dqc_reference/checkm_data
[2024-01-24 13:58:58,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:58,167] [INFO] Task started: CheckM
[2024-01-24 13:58:58,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003855255.1_ASM385525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003855255.1_ASM385525v1_genomic.fna/checkm_input GCF_003855255.1_ASM385525v1_genomic.fna/checkm_result
[2024-01-24 14:00:30,445] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:30,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:30,470] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:30,470] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:30,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003855255.1_ASM385525v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:30,471] [INFO] Task started: Blastn
[2024-01-24 14:00:30,471] [INFO] Running command: blastn -query GCF_003855255.1_ASM385525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7c9e11b-68d2-49a7-8e87-4f3b16cc1306/dqc_reference/reference_markers_gtdb.fasta -out GCF_003855255.1_ASM385525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:32,283] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:32,288] [INFO] Selected 19 target genomes.
[2024-01-24 14:00:32,288] [INFO] Target genome list was writen to GCF_003855255.1_ASM385525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:32,323] [INFO] Task started: fastANI
[2024-01-24 14:00:32,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg92ee4137-8092-4646-914c-9c7431c66f2f/GCF_003855255.1_ASM385525v1_genomic.fna.gz --refList GCF_003855255.1_ASM385525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003855255.1_ASM385525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:02,857] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:02,878] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:02,878] [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_000455325.1	s__Mycobacterium septicum	95.1638	1927	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	conclusive
GCF_004762045.1	s__Mycobacterium sp004762045	90.992	1849	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731295.1	s__Mycobacterium boenickei	89.1538	1820	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_002086835.1	s__Mycobacterium porcinum	88.957	1854	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_001245615.1	s__Mycobacterium neworleansense	88.7984	1801	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942045.1	s__Mycobacterium porcinum_A	88.5871	1693	2301	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	88.1497	1696	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000805385.1	s__Mycobacterium setense	88.0955	1725	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	98.47	0.95	0.89	4	-
GCF_001665785.1	s__Mycobacterium peregrinum_A	88.0331	1859	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665625.1	s__Mycobacterium peregrinum_B	87.9348	1709	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.32	98.32	0.89	0.89	2	-
GCF_000426065.1	s__Mycobacterium sp000426065	87.8865	1853	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102345.1	s__Mycobacterium peregrinum	87.8328	1798	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	98.27	0.94	0.91	5	-
GCF_009729095.1	s__Mycobacterium sp009729095	87.5591	1646	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_010727325.1	s__Mycobacterium alvei	87.5296	1521	2301	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	87.4792	1582	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295855.1	s__Mycobacterium fortuitum	86.8394	1686	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_900078665.2	s__Mycobacterium houstonense	86.3887	1684	2301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954135.1	s__Mycobacterium sp001954135	85.2113	1458	2301	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 14:01:02,881] [INFO] GTDB search result was written to GCF_003855255.1_ASM385525v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:02,881] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:02,886] [INFO] DFAST_QC result json was written to GCF_003855255.1_ASM385525v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:02,886] [INFO] DFAST_QC completed!
[2024-01-24 14:01:02,886] [INFO] Total running time: 0h3m5s