[2024-01-25 19:09:35,661] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:35,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:35,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg82451397-6302-49a4-92e7-5b6b514299b9/dqc_reference
[2024-01-25 19:09:36,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:36,819] [INFO] Task started: Prodigal
[2024-01-25 19:09:36,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg52139558-7ddf-4ee7-9c6e-46d82111a89d/GCF_001044255.1_ASM104425v1_genomic.fna.gz | prodigal -d GCF_001044255.1_ASM104425v1_genomic.fna/cds.fna -a GCF_001044255.1_ASM104425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:52,812] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:52,812] [INFO] Task started: HMMsearch
[2024-01-25 19:09:52,812] [INFO] Running command: hmmsearch --tblout GCF_001044255.1_ASM104425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82451397-6302-49a4-92e7-5b6b514299b9/dqc_reference/reference_markers.hmm GCF_001044255.1_ASM104425v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:53,078] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:53,079] [INFO] Found 6/6 markers.
[2024-01-25 19:09:53,128] [INFO] Query marker FASTA was written to GCF_001044255.1_ASM104425v1_genomic.fna/markers.fasta
[2024-01-25 19:09:53,128] [INFO] Task started: Blastn
[2024-01-25 19:09:53,128] [INFO] Running command: blastn -query GCF_001044255.1_ASM104425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82451397-6302-49a4-92e7-5b6b514299b9/dqc_reference/reference_markers.fasta -out GCF_001044255.1_ASM104425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:54,289] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:54,292] [INFO] Selected 10 target genomes.
[2024-01-25 19:09:54,292] [INFO] Target genome list was writen to GCF_001044255.1_ASM104425v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:54,296] [INFO] Task started: fastANI
[2024-01-25 19:09:54,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg52139558-7ddf-4ee7-9c6e-46d82111a89d/GCF_001044255.1_ASM104425v1_genomic.fna.gz --refList GCF_001044255.1_ASM104425v1_genomic.fna/target_genomes.txt --output GCF_001044255.1_ASM104425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:09,372] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:09,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82451397-6302-49a4-92e7-5b6b514299b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:09,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82451397-6302-49a4-92e7-5b6b514299b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:09,380] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:10:09,381] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:10:09,381] [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 chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	100.0	1923	1930	95	inconclusive
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	99.9813	1925	1930	95	inconclusive
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	99.9726	1891	1930	95	inconclusive
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	95.8522	1747	1930	95	inconclusive
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	95.8421	1742	1930	95	inconclusive
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.5996	1083	1930	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.5075	1069	1930	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	80.1906	934	1930	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.0112	935	1930	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.9275	897	1930	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:09,382] [INFO] DFAST Taxonomy check result was written to GCF_001044255.1_ASM104425v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:09,383] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:09,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:09,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82451397-6302-49a4-92e7-5b6b514299b9/dqc_reference/checkm_data
[2024-01-25 19:10:09,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:09,456] [INFO] Task started: CheckM
[2024-01-25 19:10:09,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001044255.1_ASM104425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001044255.1_ASM104425v1_genomic.fna/checkm_input GCF_001044255.1_ASM104425v1_genomic.fna/checkm_result
[2024-01-25 19:11:17,375] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:17,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:17,394] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:17,394] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:17,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001044255.1_ASM104425v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:17,395] [INFO] Task started: Blastn
[2024-01-25 19:11:17,395] [INFO] Running command: blastn -query GCF_001044255.1_ASM104425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82451397-6302-49a4-92e7-5b6b514299b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001044255.1_ASM104425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:19,335] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:19,338] [INFO] Selected 9 target genomes.
[2024-01-25 19:11:19,338] [INFO] Target genome list was writen to GCF_001044255.1_ASM104425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:19,343] [INFO] Task started: fastANI
[2024-01-25 19:11:19,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg52139558-7ddf-4ee7-9c6e-46d82111a89d/GCF_001044255.1_ASM104425v1_genomic.fna.gz --refList GCF_001044255.1_ASM104425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001044255.1_ASM104425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:33,369] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:33,375] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:33,375] [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_001044255.1	s__Mycobacterium chubuense	100.0	1923	1930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	conclusive
GCF_001044235.1	s__Mycobacterium chlorophenolicum	95.8522	1747	1930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	91.102	1591	1930	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	89.2866	1661	1930	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	84.1902	1355	1930	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	84.1361	1301	1930	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	82.8579	1041	1930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570325.1	s__Mycobacterium sp004570325	81.5115	1087	1930	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	80.3393	984	1930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:33,377] [INFO] GTDB search result was written to GCF_001044255.1_ASM104425v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:33,377] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:33,380] [INFO] DFAST_QC result json was written to GCF_001044255.1_ASM104425v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:33,381] [INFO] DFAST_QC completed!
[2024-01-25 19:11:33,381] [INFO] Total running time: 0h1m58s