[2024-01-25 20:22:50,582] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:50,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:50,584] [INFO] DQC Reference Directory: /var/lib/cwl/stgefdd2868-b8e1-43ad-acc2-1fb07b4448c1/dqc_reference
[2024-01-25 20:22:51,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:51,788] [INFO] Task started: Prodigal
[2024-01-25 20:22:51,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg213f44f6-9be8-4ff1-9472-91fd3551f656/GCF_002101675.1_ASM210167v1_genomic.fna.gz | prodigal -d GCF_002101675.1_ASM210167v1_genomic.fna/cds.fna -a GCF_002101675.1_ASM210167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:14,558] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:14,559] [INFO] Task started: HMMsearch
[2024-01-25 20:23:14,559] [INFO] Running command: hmmsearch --tblout GCF_002101675.1_ASM210167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefdd2868-b8e1-43ad-acc2-1fb07b4448c1/dqc_reference/reference_markers.hmm GCF_002101675.1_ASM210167v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:14,953] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:14,954] [INFO] Found 6/6 markers.
[2024-01-25 20:23:15,072] [INFO] Query marker FASTA was written to GCF_002101675.1_ASM210167v1_genomic.fna/markers.fasta
[2024-01-25 20:23:15,072] [INFO] Task started: Blastn
[2024-01-25 20:23:15,072] [INFO] Running command: blastn -query GCF_002101675.1_ASM210167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefdd2868-b8e1-43ad-acc2-1fb07b4448c1/dqc_reference/reference_markers.fasta -out GCF_002101675.1_ASM210167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:16,108] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:16,110] [INFO] Selected 14 target genomes.
[2024-01-25 20:23:16,111] [INFO] Target genome list was writen to GCF_002101675.1_ASM210167v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:16,119] [INFO] Task started: fastANI
[2024-01-25 20:23:16,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg213f44f6-9be8-4ff1-9472-91fd3551f656/GCF_002101675.1_ASM210167v1_genomic.fna.gz --refList GCF_002101675.1_ASM210167v1_genomic.fna/target_genomes.txt --output GCF_002101675.1_ASM210167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:40,879] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:40,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefdd2868-b8e1-43ad-acc2-1fb07b4448c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:40,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefdd2868-b8e1-43ad-acc2-1fb07b4448c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:40,890] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:40,890] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:40,890] [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
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	100.0	2387	2401	95	conclusive
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	86.8926	1807	2401	95	below_threshold
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	86.8252	1825	2401	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_002086545.1	1790	1790	suspected-type	True	81.6545	1312	2401	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_000613245.1	1790	1790	suspected-type	True	81.5663	1327	2401	95	below_threshold
Mycobacterium vicinigordonae	strain=24	GCA_013466425.1	1719132	1719132	type	True	81.1084	1214	2401	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	81.0775	1122	2401	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	80.7917	1220	2401	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	80.7007	1241	2401	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	80.6863	918	2401	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.5789	1064	2401	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	80.5109	1114	2401	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	80.3344	1114	2401	95	below_threshold
Mycobacterium kansasii	strain=ATCC 12478	GCA_000157895.2	1768	1768	type	True	80.0648	1156	2401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:40,891] [INFO] DFAST Taxonomy check result was written to GCF_002101675.1_ASM210167v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:40,892] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:40,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:40,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefdd2868-b8e1-43ad-acc2-1fb07b4448c1/dqc_reference/checkm_data
[2024-01-25 20:23:40,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:40,963] [INFO] Task started: CheckM
[2024-01-25 20:23:40,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101675.1_ASM210167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101675.1_ASM210167v1_genomic.fna/checkm_input GCF_002101675.1_ASM210167v1_genomic.fna/checkm_result
[2024-01-25 20:24:45,105] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:45,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:45,131] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:45,131] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:45,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101675.1_ASM210167v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:45,132] [INFO] Task started: Blastn
[2024-01-25 20:24:45,132] [INFO] Running command: blastn -query GCF_002101675.1_ASM210167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefdd2868-b8e1-43ad-acc2-1fb07b4448c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101675.1_ASM210167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:46,632] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:46,636] [INFO] Selected 10 target genomes.
[2024-01-25 20:24:46,636] [INFO] Target genome list was writen to GCF_002101675.1_ASM210167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:46,646] [INFO] Task started: fastANI
[2024-01-25 20:24:46,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg213f44f6-9be8-4ff1-9472-91fd3551f656/GCF_002101675.1_ASM210167v1_genomic.fna.gz --refList GCF_002101675.1_ASM210167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101675.1_ASM210167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:08,271] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:08,279] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:08,279] [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_002101675.1	s__Mycobacterium gordonae	100.0	2388	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	conclusive
GCF_017086405.1	s__Mycobacterium gordonae_D	87.7664	1821	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417955.2	s__Mycobacterium gordonae_B	87.329	1794	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614435.1	s__Mycobacterium paragordonae	86.8321	1824	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCA_003987775.1	s__Mycobacterium sp003987775	86.1497	1797	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466425.1	s__Mycobacterium vicinigordonae	81.1136	1213	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086155.1	s__Mycobacterium angelicum	80.79	1220	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002116635.1	s__Mycobacterium szulgai	80.7001	1240	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705925.1	s__Mycobacterium ostraviense	80.3664	1108	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_010723575.1	s__Mycobacterium bourgelatii	80.2768	1238	2401	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 20:25:08,280] [INFO] GTDB search result was written to GCF_002101675.1_ASM210167v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:08,281] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:08,283] [INFO] DFAST_QC result json was written to GCF_002101675.1_ASM210167v1_genomic.fna/dqc_result.json
[2024-01-25 20:25:08,284] [INFO] DFAST_QC completed!
[2024-01-25 20:25:08,284] [INFO] Total running time: 0h2m18s