[2024-01-24 12:29:28,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg896339ea-7da2-4844-8dba-5c5aeb75fac1/dqc_reference
[2024-01-24 12:29:30,327] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,328] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,328] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a3bd751-183c-46b9-8326-c5a274214c0d/GCF_002086115.1_ASM208611v1_genomic.fna.gz | prodigal -d GCF_002086115.1_ASM208611v1_genomic.fna/cds.fna -a GCF_002086115.1_ASM208611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:50,391] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:50,391] [INFO] Task started: HMMsearch
[2024-01-24 12:29:50,391] [INFO] Running command: hmmsearch --tblout GCF_002086115.1_ASM208611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg896339ea-7da2-4844-8dba-5c5aeb75fac1/dqc_reference/reference_markers.hmm GCF_002086115.1_ASM208611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:50,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:50,807] [INFO] Found 6/6 markers.
[2024-01-24 12:29:50,881] [INFO] Query marker FASTA was written to GCF_002086115.1_ASM208611v1_genomic.fna/markers.fasta
[2024-01-24 12:29:50,882] [INFO] Task started: Blastn
[2024-01-24 12:29:50,882] [INFO] Running command: blastn -query GCF_002086115.1_ASM208611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg896339ea-7da2-4844-8dba-5c5aeb75fac1/dqc_reference/reference_markers.fasta -out GCF_002086115.1_ASM208611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:52,235] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:52,239] [INFO] Selected 17 target genomes.
[2024-01-24 12:29:52,240] [INFO] Target genome list was writen to GCF_002086115.1_ASM208611v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:52,249] [INFO] Task started: fastANI
[2024-01-24 12:29:52,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a3bd751-183c-46b9-8326-c5a274214c0d/GCF_002086115.1_ASM208611v1_genomic.fna.gz --refList GCF_002086115.1_ASM208611v1_genomic.fna/target_genomes.txt --output GCF_002086115.1_ASM208611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:17,181] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:17,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg896339ea-7da2-4844-8dba-5c5aeb75fac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:17,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg896339ea-7da2-4844-8dba-5c5aeb75fac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:17,198] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:17,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:17,199] [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 bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	100.0	1944	1946	95	conclusive
Mycolicibacterium neoaurum	strain=ATCC 25795	GCA_000691525.1	1795	1795	type	True	85.4954	1416	1946	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	85.4363	1420	1946	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_000724065.1	1795	1795	type	True	85.4165	1405	1946	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	82.0463	1186	1946	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	81.9032	1101	1946	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	81.5433	1108	1946	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.7917	1040	1946	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.307	970	1946	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	80.1989	978	1946	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	80.1848	949	1946	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.0674	1036	1946	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.0561	1022	1946	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	80.0408	1046	1946	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.8809	832	1946	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.7844	864	1946	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6408	874	1946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:17,202] [INFO] DFAST Taxonomy check result was written to GCF_002086115.1_ASM208611v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:17,203] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:17,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:17,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg896339ea-7da2-4844-8dba-5c5aeb75fac1/dqc_reference/checkm_data
[2024-01-24 12:30:17,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:17,269] [INFO] Task started: CheckM
[2024-01-24 12:30:17,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086115.1_ASM208611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086115.1_ASM208611v1_genomic.fna/checkm_input GCF_002086115.1_ASM208611v1_genomic.fna/checkm_result
[2024-01-24 12:31:23,073] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:23,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:23,100] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:23,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:23,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086115.1_ASM208611v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:23,101] [INFO] Task started: Blastn
[2024-01-24 12:31:23,101] [INFO] Running command: blastn -query GCF_002086115.1_ASM208611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg896339ea-7da2-4844-8dba-5c5aeb75fac1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086115.1_ASM208611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:25,229] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:25,234] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:25,234] [INFO] Target genome list was writen to GCF_002086115.1_ASM208611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:25,258] [INFO] Task started: fastANI
[2024-01-24 12:31:25,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a3bd751-183c-46b9-8326-c5a274214c0d/GCF_002086115.1_ASM208611v1_genomic.fna.gz --refList GCF_002086115.1_ASM208611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086115.1_ASM208611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:46,852] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:46,865] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:46,865] [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_002086115.1	s__Mycobacterium bacteremicum	100.0	1944	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000691525.1	s__Mycobacterium neoaurum	85.4936	1416	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	98.36	0.96	0.91	6	-
GCF_000317305.3	s__Mycobacterium neoaurum_A	85.3959	1376	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_900078775.1	s__Mycobacterium aurum_A	83.5578	1350	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428895.1	s__Mycobacterium sp001428895	83.4343	1502	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644575.1	s__Mycobacterium sp001644575	83.2542	1329	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.69	99.69	0.98	0.98	2	-
GCF_001907655.1	s__Mycobacterium diernhoferi	83.2531	1284	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_008329585.1	s__Mycobacterium sp008329585	83.1479	1418	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613185.1	s__Mycobacterium cosmeticum	81.971	1205	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_002101555.1	s__Mycobacterium canariasense	81.9337	1102	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001245615.1	s__Mycobacterium neworleansense	80.5289	1024	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086485.1	s__Mycobacterium aquaticum	80.199	946	1946	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	80.1985	978	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665685.1	s__Mycobacterium sp001665685	80.0583	959	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552615.1	s__Millisia brevis	77.6495	433	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Millisia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:46,867] [INFO] GTDB search result was written to GCF_002086115.1_ASM208611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:46,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:46,872] [INFO] DFAST_QC result json was written to GCF_002086115.1_ASM208611v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:46,872] [INFO] DFAST_QC completed!
[2024-01-24 12:31:46,872] [INFO] Total running time: 0h2m18s