[2024-01-24 11:19:48,976] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:48,978] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:48,978] [INFO] DQC Reference Directory: /var/lib/cwl/stg3268d328-3502-420a-baae-373b73121b99/dqc_reference
[2024-01-24 11:19:50,163] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:50,164] [INFO] Task started: Prodigal
[2024-01-24 11:19:50,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg24c45ba1-a7c6-49a2-b82d-826caad71446/GCF_012396425.1_ASM1239642v1_genomic.fna.gz | prodigal -d GCF_012396425.1_ASM1239642v1_genomic.fna/cds.fna -a GCF_012396425.1_ASM1239642v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:18,081] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:18,081] [INFO] Task started: HMMsearch
[2024-01-24 11:20:18,082] [INFO] Running command: hmmsearch --tblout GCF_012396425.1_ASM1239642v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3268d328-3502-420a-baae-373b73121b99/dqc_reference/reference_markers.hmm GCF_012396425.1_ASM1239642v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:18,416] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:18,418] [INFO] Found 6/6 markers.
[2024-01-24 11:20:18,479] [INFO] Query marker FASTA was written to GCF_012396425.1_ASM1239642v1_genomic.fna/markers.fasta
[2024-01-24 11:20:18,479] [INFO] Task started: Blastn
[2024-01-24 11:20:18,480] [INFO] Running command: blastn -query GCF_012396425.1_ASM1239642v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3268d328-3502-420a-baae-373b73121b99/dqc_reference/reference_markers.fasta -out GCF_012396425.1_ASM1239642v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:19,652] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:19,655] [INFO] Selected 16 target genomes.
[2024-01-24 11:20:19,656] [INFO] Target genome list was writen to GCF_012396425.1_ASM1239642v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:19,662] [INFO] Task started: fastANI
[2024-01-24 11:20:19,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg24c45ba1-a7c6-49a2-b82d-826caad71446/GCF_012396425.1_ASM1239642v1_genomic.fna.gz --refList GCF_012396425.1_ASM1239642v1_genomic.fna/target_genomes.txt --output GCF_012396425.1_ASM1239642v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:44,323] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:44,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3268d328-3502-420a-baae-373b73121b99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:44,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3268d328-3502-420a-baae-373b73121b99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:44,340] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:20:44,340] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:20:44,340] [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 septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	100.0	2281	2283	95	inconclusive
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	99.9741	2280	2283	95	inconclusive
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	95.1129	1924	2283	95	inconclusive
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	89.1935	1804	2283	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	88.9839	1811	2283	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	88.0383	1699	2283	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	87.6351	1605	2283	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	87.5766	1692	2283	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	87.5431	1522	2283	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	87.0165	1642	2283	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	86.9609	1675	2283	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	86.9341	1682	2283	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.5672	940	2283	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6115	932	2283	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.5747	938	2283	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.5313	939	2283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:44,342] [INFO] DFAST Taxonomy check result was written to GCF_012396425.1_ASM1239642v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:44,342] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:44,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:44,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3268d328-3502-420a-baae-373b73121b99/dqc_reference/checkm_data
[2024-01-24 11:20:44,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:44,408] [INFO] Task started: CheckM
[2024-01-24 11:20:44,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396425.1_ASM1239642v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396425.1_ASM1239642v1_genomic.fna/checkm_input GCF_012396425.1_ASM1239642v1_genomic.fna/checkm_result
[2024-01-24 11:22:06,613] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:06,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:06,639] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:06,639] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:06,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396425.1_ASM1239642v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:06,640] [INFO] Task started: Blastn
[2024-01-24 11:22:06,640] [INFO] Running command: blastn -query GCF_012396425.1_ASM1239642v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3268d328-3502-420a-baae-373b73121b99/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396425.1_ASM1239642v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:08,370] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:08,375] [INFO] Selected 16 target genomes.
[2024-01-24 11:22:08,375] [INFO] Target genome list was writen to GCF_012396425.1_ASM1239642v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:08,388] [INFO] Task started: fastANI
[2024-01-24 11:22:08,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg24c45ba1-a7c6-49a2-b82d-826caad71446/GCF_012396425.1_ASM1239642v1_genomic.fna.gz --refList GCF_012396425.1_ASM1239642v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396425.1_ASM1239642v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:33,765] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:33,791] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:33,791] [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	99.9741	2280	2283	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	90.8521	1775	2283	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	89.1736	1808	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_001245615.1	s__Mycobacterium neworleansense	88.9839	1811	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086835.1	s__Mycobacterium porcinum	88.8959	1788	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_001942045.1	s__Mycobacterium porcinum_A	88.6213	1712	2283	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	88.2738	1668	2283	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	88.0419	1698	2283	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	87.9911	1756	2283	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	87.6351	1605	2283	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	87.6003	1609	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_010727325.1	s__Mycobacterium alvei	87.5502	1521	2283	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	87.0165	1642	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_001954135.1	s__Mycobacterium sp001954135	85.3914	1468	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	82.4462	1396	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_001665685.1	s__Mycobacterium sp001665685	81.8935	1270	2283	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 11:22:33,792] [INFO] GTDB search result was written to GCF_012396425.1_ASM1239642v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:33,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:33,796] [INFO] DFAST_QC result json was written to GCF_012396425.1_ASM1239642v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:33,796] [INFO] DFAST_QC completed!
[2024-01-24 11:22:33,797] [INFO] Total running time: 0h2m45s