[2024-01-24 15:18:18,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7fc561a-e8cd-4df2-add2-34532ab408d8/dqc_reference
[2024-01-24 15:18:19,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:19,951] [INFO] Task started: Prodigal
[2024-01-24 15:18:19,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b0093db-0fba-45ff-bc2b-a8ebc5288388/GCF_001044235.1_ASM104423v1_genomic.fna.gz | prodigal -d GCF_001044235.1_ASM104423v1_genomic.fna/cds.fna -a GCF_001044235.1_ASM104423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:50,280] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:50,281] [INFO] Task started: HMMsearch
[2024-01-24 15:18:50,281] [INFO] Running command: hmmsearch --tblout GCF_001044235.1_ASM104423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7fc561a-e8cd-4df2-add2-34532ab408d8/dqc_reference/reference_markers.hmm GCF_001044235.1_ASM104423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:50,692] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:50,694] [INFO] Found 6/6 markers.
[2024-01-24 15:18:50,755] [INFO] Query marker FASTA was written to GCF_001044235.1_ASM104423v1_genomic.fna/markers.fasta
[2024-01-24 15:18:50,755] [INFO] Task started: Blastn
[2024-01-24 15:18:50,755] [INFO] Running command: blastn -query GCF_001044235.1_ASM104423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7fc561a-e8cd-4df2-add2-34532ab408d8/dqc_reference/reference_markers.fasta -out GCF_001044235.1_ASM104423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:52,000] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:52,003] [INFO] Selected 16 target genomes.
[2024-01-24 15:18:52,004] [INFO] Target genome list was writen to GCF_001044235.1_ASM104423v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:52,011] [INFO] Task started: fastANI
[2024-01-24 15:18:52,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b0093db-0fba-45ff-bc2b-a8ebc5288388/GCF_001044235.1_ASM104423v1_genomic.fna.gz --refList GCF_001044235.1_ASM104423v1_genomic.fna/target_genomes.txt --output GCF_001044235.1_ASM104423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:16,514] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:16,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7fc561a-e8cd-4df2-add2-34532ab408d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:16,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7fc561a-e8cd-4df2-add2-34532ab408d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:16,534] [INFO] Found 16 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 15:19:16,534] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:19:16,534] [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 chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	100.0	2417	2421	95	inconclusive
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	99.9704	2364	2421	95	inconclusive
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	95.8163	1758	2421	95	inconclusive
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	95.8155	1749	2421	95	inconclusive
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	95.7331	1799	2421	95	inconclusive
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	91.3199	1614	2421	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.6541	1125	2421	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.4916	1142	2421	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	80.2969	1039	2421	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.0326	923	2421	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.9941	979	2421	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.9362	954	2421	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	79.8789	1022	2421	95	below_threshold
Mycobacteroides saopaulense	strain=EPM10906	GCA_001456355.1	1578165	1578165	type	True	78.454	469	2421	95	below_threshold
Pseudonocardia thermophila	strain=DSM 43832	GCA_900142365.1	1848	1848	type	True	76.6695	549	2421	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	76.5744	529	2421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:16,536] [INFO] DFAST Taxonomy check result was written to GCF_001044235.1_ASM104423v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:16,537] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:16,537] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:16,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7fc561a-e8cd-4df2-add2-34532ab408d8/dqc_reference/checkm_data
[2024-01-24 15:19:16,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:16,627] [INFO] Task started: CheckM
[2024-01-24 15:19:16,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001044235.1_ASM104423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001044235.1_ASM104423v1_genomic.fna/checkm_input GCF_001044235.1_ASM104423v1_genomic.fna/checkm_result
[2024-01-24 15:20:57,450] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:57,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:57,485] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:57,485] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:57,486] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001044235.1_ASM104423v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:57,486] [INFO] Task started: Blastn
[2024-01-24 15:20:57,486] [INFO] Running command: blastn -query GCF_001044235.1_ASM104423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7fc561a-e8cd-4df2-add2-34532ab408d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001044235.1_ASM104423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:59,322] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:59,327] [INFO] Selected 13 target genomes.
[2024-01-24 15:20:59,327] [INFO] Target genome list was writen to GCF_001044235.1_ASM104423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:59,338] [INFO] Task started: fastANI
[2024-01-24 15:20:59,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b0093db-0fba-45ff-bc2b-a8ebc5288388/GCF_001044235.1_ASM104423v1_genomic.fna.gz --refList GCF_001044235.1_ASM104423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001044235.1_ASM104423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:19,949] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:19,964] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:19,964] [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_001044235.1	s__Mycobacterium chlorophenolicum	100.0	2417	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	conclusive
GCF_001044255.1	s__Mycobacterium chubuense	95.8155	1749	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	91.3293	1613	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
GCA_000762985.1	s__Mycobacterium rufum_A	89.2638	1723	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044245.1	s__Mycobacterium obuense	84.4178	1408	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	-
GCF_007096635.1	s__Mycobacterium sp007096635	84.2611	1365	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	82.9384	1054	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328565.1	s__Mycobacterium sp000328565	80.8449	1022	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050035.1	s__Mycobacterium komanii	80.8379	1015	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723835.1	s__Mycobacterium sp002723835	80.7131	1038	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729665.1	s__Mycobacterium madagascariense	80.5894	1006	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243415.2	s__Mycobacterium tusciae_A	80.318	1030	2421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	80.2711	1044	2421	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 15:21:19,966] [INFO] GTDB search result was written to GCF_001044235.1_ASM104423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:19,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:19,970] [INFO] DFAST_QC result json was written to GCF_001044235.1_ASM104423v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:19,970] [INFO] DFAST_QC completed!
[2024-01-24 15:21:19,970] [INFO] Total running time: 0h3m1s