[2024-01-24 12:37:09,464] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,471] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc2b6a3c-6b14-45d6-82ef-8d8d416d06c1/dqc_reference
[2024-01-24 12:37:10,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:10,854] [INFO] Task started: Prodigal
[2024-01-24 12:37:10,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg550c90cf-a7f3-4b75-aaf4-cbd9fadd69aa/GCF_002086815.1_ASM208681v1_genomic.fna.gz | prodigal -d GCF_002086815.1_ASM208681v1_genomic.fna/cds.fna -a GCF_002086815.1_ASM208681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:28,950] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:28,950] [INFO] Task started: HMMsearch
[2024-01-24 12:37:28,951] [INFO] Running command: hmmsearch --tblout GCF_002086815.1_ASM208681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc2b6a3c-6b14-45d6-82ef-8d8d416d06c1/dqc_reference/reference_markers.hmm GCF_002086815.1_ASM208681v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:29,273] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:29,275] [INFO] Found 6/6 markers.
[2024-01-24 12:37:29,327] [INFO] Query marker FASTA was written to GCF_002086815.1_ASM208681v1_genomic.fna/markers.fasta
[2024-01-24 12:37:29,328] [INFO] Task started: Blastn
[2024-01-24 12:37:29,328] [INFO] Running command: blastn -query GCF_002086815.1_ASM208681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc2b6a3c-6b14-45d6-82ef-8d8d416d06c1/dqc_reference/reference_markers.fasta -out GCF_002086815.1_ASM208681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:30,672] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:30,677] [INFO] Selected 22 target genomes.
[2024-01-24 12:37:30,677] [INFO] Target genome list was writen to GCF_002086815.1_ASM208681v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:30,689] [INFO] Task started: fastANI
[2024-01-24 12:37:30,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg550c90cf-a7f3-4b75-aaf4-cbd9fadd69aa/GCF_002086815.1_ASM208681v1_genomic.fna.gz --refList GCF_002086815.1_ASM208681v1_genomic.fna/target_genomes.txt --output GCF_002086815.1_ASM208681v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:59,453] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:59,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc2b6a3c-6b14-45d6-82ef-8d8d416d06c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:59,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc2b6a3c-6b14-45d6-82ef-8d8d416d06c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:59,478] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:59,478] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:59,478] [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 vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	83.8313	1344	2009	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	83.8141	1489	2009	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	82.6843	1281	2009	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	82.6461	1244	2009	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	82.6327	1271	2009	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	82.5379	1217	2009	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	82.3405	1370	2009	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	82.2973	1383	2009	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	82.037	1163	2009	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	82.0315	1176	2009	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.9702	1187	2009	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	81.1581	1092	2009	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	81.1483	1102	2009	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	81.0456	1139	2009	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.3036	1011	2009	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	80.0808	1048	2009	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.0202	1050	2009	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.02	940	2009	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.8592	947	2009	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.8492	931	2009	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.8065	891	2009	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.7415	916	2009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:59,480] [INFO] DFAST Taxonomy check result was written to GCF_002086815.1_ASM208681v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:59,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:59,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:59,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc2b6a3c-6b14-45d6-82ef-8d8d416d06c1/dqc_reference/checkm_data
[2024-01-24 12:37:59,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:59,548] [INFO] Task started: CheckM
[2024-01-24 12:37:59,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086815.1_ASM208681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086815.1_ASM208681v1_genomic.fna/checkm_input GCF_002086815.1_ASM208681v1_genomic.fna/checkm_result
[2024-01-24 12:38:58,852] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:58,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:58,877] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:58,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:58,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086815.1_ASM208681v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:58,878] [INFO] Task started: Blastn
[2024-01-24 12:38:58,878] [INFO] Running command: blastn -query GCF_002086815.1_ASM208681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc2b6a3c-6b14-45d6-82ef-8d8d416d06c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086815.1_ASM208681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:01,101] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:01,106] [INFO] Selected 13 target genomes.
[2024-01-24 12:39:01,106] [INFO] Target genome list was writen to GCF_002086815.1_ASM208681v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:01,122] [INFO] Task started: fastANI
[2024-01-24 12:39:01,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg550c90cf-a7f3-4b75-aaf4-cbd9fadd69aa/GCF_002086815.1_ASM208681v1_genomic.fna.gz --refList GCF_002086815.1_ASM208681v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086815.1_ASM208681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:20,042] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:20,065] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:20,065] [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_002086815.1	s__Mycobacterium parafortuitum	100.0	2005	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_010725485.1	s__Mycobacterium sp002946335	94.7423	1847	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.86	98.86	0.96	0.96	2	-
GCF_900454025.1	s__Mycobacterium gilvum	84.7097	1475	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_001545925.1	s__Mycobacterium sp001545925	83.906	1141	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552715.1	s__Mycobacterium vaccae	83.8351	1343	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_000612725.1	s__Mycobacterium austroafricanum	83.58	1371	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_014190915.1	s__Mycobacterium iranicum_B	83.2553	1322	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000762985.1	s__Mycobacterium rufum_A	82.5598	1250	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	81.9468	1191	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_900108565.1	s__Mycobacterium rutilum	81.7477	1136	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007096635.1	s__Mycobacterium sp007096635	81.7437	1114	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187505.1	s__Mycobacterium goodii_B	80.7202	1093	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637205.1	s__Mycobacterium chitae	80.5774	1006	2009	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:20,067] [INFO] GTDB search result was written to GCF_002086815.1_ASM208681v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:20,068] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:20,072] [INFO] DFAST_QC result json was written to GCF_002086815.1_ASM208681v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:20,072] [INFO] DFAST_QC completed!
[2024-01-24 12:39:20,072] [INFO] Total running time: 0h2m11s