[2024-01-24 12:52:24,785] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:24,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:24,788] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8dfcd23-ae1c-469b-ad7b-523d396fb675/dqc_reference
[2024-01-24 12:52:26,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:26,097] [INFO] Task started: Prodigal
[2024-01-24 12:52:26,098] [INFO] Running command: gunzip -c /var/lib/cwl/stg90c0300f-0ef2-4374-9b4f-84ed261a8d62/GCF_002086595.1_ASM208659v1_genomic.fna.gz | prodigal -d GCF_002086595.1_ASM208659v1_genomic.fna/cds.fna -a GCF_002086595.1_ASM208659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:45,741] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:45,741] [INFO] Task started: HMMsearch
[2024-01-24 12:52:45,741] [INFO] Running command: hmmsearch --tblout GCF_002086595.1_ASM208659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8dfcd23-ae1c-469b-ad7b-523d396fb675/dqc_reference/reference_markers.hmm GCF_002086595.1_ASM208659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:46,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:46,137] [INFO] Found 6/6 markers.
[2024-01-24 12:52:46,196] [INFO] Query marker FASTA was written to GCF_002086595.1_ASM208659v1_genomic.fna/markers.fasta
[2024-01-24 12:52:46,196] [INFO] Task started: Blastn
[2024-01-24 12:52:46,196] [INFO] Running command: blastn -query GCF_002086595.1_ASM208659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8dfcd23-ae1c-469b-ad7b-523d396fb675/dqc_reference/reference_markers.fasta -out GCF_002086595.1_ASM208659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:47,463] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:47,466] [INFO] Selected 16 target genomes.
[2024-01-24 12:52:47,466] [INFO] Target genome list was writen to GCF_002086595.1_ASM208659v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:47,485] [INFO] Task started: fastANI
[2024-01-24 12:52:47,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg90c0300f-0ef2-4374-9b4f-84ed261a8d62/GCF_002086595.1_ASM208659v1_genomic.fna.gz --refList GCF_002086595.1_ASM208659v1_genomic.fna/target_genomes.txt --output GCF_002086595.1_ASM208659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:07,237] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:07,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8dfcd23-ae1c-469b-ad7b-523d396fb675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:07,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8dfcd23-ae1c-469b-ad7b-523d396fb675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:07,257] [INFO] Found 16 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:53:07,257] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:53:07,258] [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_002086595.1	1800	1800	type	True	100.0	1942	1945	95	inconclusive
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	99.9924	1942	1945	95	inconclusive
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	99.9636	1906	1945	95	inconclusive
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	95.8873	1754	1945	95	inconclusive
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	95.8796	1767	1945	95	inconclusive
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	91.1295	1594	1945	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.6719	1075	1945	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.5375	1081	1945	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	80.0701	952	1945	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.9415	947	1945	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.8837	921	1945	95	below_threshold
Mycobacterium tuberculosis variant pinnipedii	strain=ATCC BAA-688	GCA_002982275.1	194542	1773	type	True	78.1672	503	1945	95	below_threshold
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	78.1501	483	1945	95	below_threshold
Mycobacterium tuberculosis variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	78.1201	513	1945	95	below_threshold
Mycobacterium tuberculosis variant bovis	strain=ATCC 19210	GCA_002982285.1	1765	1773	type	True	78.1019	482	1945	95	below_threshold
Mycobacterium tuberculosis variant caprae	strain=ATCC BAA-824	GCA_002982225.1	115862	1773	type	True	78.0803	509	1945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:07,259] [INFO] DFAST Taxonomy check result was written to GCF_002086595.1_ASM208659v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:07,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:07,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:07,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8dfcd23-ae1c-469b-ad7b-523d396fb675/dqc_reference/checkm_data
[2024-01-24 12:53:07,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:07,315] [INFO] Task started: CheckM
[2024-01-24 12:53:07,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086595.1_ASM208659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086595.1_ASM208659v1_genomic.fna/checkm_input GCF_002086595.1_ASM208659v1_genomic.fna/checkm_result
[2024-01-24 12:54:14,025] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:14,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.85%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:14,061] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:14,061] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:14,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086595.1_ASM208659v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:14,062] [INFO] Task started: Blastn
[2024-01-24 12:54:14,062] [INFO] Running command: blastn -query GCF_002086595.1_ASM208659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8dfcd23-ae1c-469b-ad7b-523d396fb675/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086595.1_ASM208659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:15,781] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:15,785] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:15,786] [INFO] Target genome list was writen to GCF_002086595.1_ASM208659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:15,817] [INFO] Task started: fastANI
[2024-01-24 12:54:15,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg90c0300f-0ef2-4374-9b4f-84ed261a8d62/GCF_002086595.1_ASM208659v1_genomic.fna.gz --refList GCF_002086595.1_ASM208659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086595.1_ASM208659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:32,635] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:32,646] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:54:32,646] [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	99.9636	1906	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	inconclusive
GCF_001044235.1	s__Mycobacterium chlorophenolicum	95.8676	1768	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	inconclusive
GCF_010729305.1	s__Mycobacterium psychrotolerans	91.1352	1593	1945	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	89.2424	1689	1945	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	84.1618	1373	1945	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	84.1085	1322	1945	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	81.5738	1090	1945	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	80.3533	987	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	79.5425	780	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665295.1	s__Mycobacterium sp001665295	79.358	802	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455205.1	s__Mycobacterium sp000455205	79.3368	789	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.16	95.96	0.85	0.84	3	-
GCF_000195955.2	s__Mycobacterium tuberculosis	78.0989	527	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:32,648] [INFO] GTDB search result was written to GCF_002086595.1_ASM208659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:32,649] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:32,652] [INFO] DFAST_QC result json was written to GCF_002086595.1_ASM208659v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:32,652] [INFO] DFAST_QC completed!
[2024-01-24 12:54:32,652] [INFO] Total running time: 0h2m8s