[2024-01-25 18:51:50,574] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:50,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:50,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fc4dba5-ada0-4cac-b1da-09315117d8ba/dqc_reference
[2024-01-25 18:51:51,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:51,792] [INFO] Task started: Prodigal
[2024-01-25 18:51:51,792] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0c9aaf8-9004-42f6-a019-f8074aa0fea6/GCF_016313185.1_ASM1631318v1_genomic.fna.gz | prodigal -d GCF_016313185.1_ASM1631318v1_genomic.fna/cds.fna -a GCF_016313185.1_ASM1631318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:09,123] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:09,123] [INFO] Task started: HMMsearch
[2024-01-25 18:52:09,123] [INFO] Running command: hmmsearch --tblout GCF_016313185.1_ASM1631318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fc4dba5-ada0-4cac-b1da-09315117d8ba/dqc_reference/reference_markers.hmm GCF_016313185.1_ASM1631318v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:09,444] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:09,445] [INFO] Found 6/6 markers.
[2024-01-25 18:52:09,496] [INFO] Query marker FASTA was written to GCF_016313185.1_ASM1631318v1_genomic.fna/markers.fasta
[2024-01-25 18:52:09,496] [INFO] Task started: Blastn
[2024-01-25 18:52:09,496] [INFO] Running command: blastn -query GCF_016313185.1_ASM1631318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fc4dba5-ada0-4cac-b1da-09315117d8ba/dqc_reference/reference_markers.fasta -out GCF_016313185.1_ASM1631318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:10,617] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:10,620] [INFO] Selected 12 target genomes.
[2024-01-25 18:52:10,620] [INFO] Target genome list was writen to GCF_016313185.1_ASM1631318v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:10,631] [INFO] Task started: fastANI
[2024-01-25 18:52:10,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0c9aaf8-9004-42f6-a019-f8074aa0fea6/GCF_016313185.1_ASM1631318v1_genomic.fna.gz --refList GCF_016313185.1_ASM1631318v1_genomic.fna/target_genomes.txt --output GCF_016313185.1_ASM1631318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:26,147] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:26,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fc4dba5-ada0-4cac-b1da-09315117d8ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:26,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fc4dba5-ada0-4cac-b1da-09315117d8ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:26,157] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:52:26,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:26,158] [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 baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	100.0	2058	2060	95	conclusive
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	99.989	2041	2060	95	conclusive
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	87.3736	1501	2060	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	87.3698	1498	2060	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	86.5861	1425	2060	95	below_threshold
Mycobacterium doricum	strain=JCM 12405	GCA_010728155.1	126673	126673	type	True	85.1417	982	2060	95	below_threshold
Mycobacterium doricum	strain=DSM 44339	GCA_002102115.1	126673	126673	type	True	85.035	965	2060	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	80.1056	958	2060	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	80.0207	985	2060	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.9257	914	2060	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.537	878	2060	95	below_threshold
Mycobacteroides abscessus subsp. massiliense	strain=CCUG 48898	GCA_000239055.2	1962118	36809	type	True	77.9137	395	2060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:26,159] [INFO] DFAST Taxonomy check result was written to GCF_016313185.1_ASM1631318v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:26,160] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:26,160] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:26,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fc4dba5-ada0-4cac-b1da-09315117d8ba/dqc_reference/checkm_data
[2024-01-25 18:52:26,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:26,219] [INFO] Task started: CheckM
[2024-01-25 18:52:26,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016313185.1_ASM1631318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016313185.1_ASM1631318v1_genomic.fna/checkm_input GCF_016313185.1_ASM1631318v1_genomic.fna/checkm_result
[2024-01-25 18:53:48,139] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:48,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:48,154] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:48,154] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:48,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016313185.1_ASM1631318v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:48,155] [INFO] Task started: Blastn
[2024-01-25 18:53:48,155] [INFO] Running command: blastn -query GCF_016313185.1_ASM1631318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fc4dba5-ada0-4cac-b1da-09315117d8ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_016313185.1_ASM1631318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:49,866] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:49,869] [INFO] Selected 15 target genomes.
[2024-01-25 18:53:49,869] [INFO] Target genome list was writen to GCF_016313185.1_ASM1631318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:49,879] [INFO] Task started: fastANI
[2024-01-25 18:53:49,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0c9aaf8-9004-42f6-a019-f8074aa0fea6/GCF_016313185.1_ASM1631318v1_genomic.fna.gz --refList GCF_016313185.1_ASM1631318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016313185.1_ASM1631318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:10,382] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:10,392] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:10,392] [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_016313185.1	s__Mycobacterium sp016313185	100.0	2058	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	conclusive
GCF_010731695.1	s__Mycobacterium litorale	87.3825	1501	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014218295.1	s__Mycobacterium litorale_B	86.6083	1502	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731575.1	s__Mycobacterium monacense	86.5657	1435	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	-
GCF_001499995.1	s__Mycobacterium sp001499995	86.4162	1384	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500125.1	s__Mycobacterium sp001500125	86.197	1383	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010728155.1	s__Mycobacterium doricum	85.1522	981	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001499965.1	s__Mycobacterium sp001499965	85.0366	1444	2060	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	83.319	1231	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665575.1	s__Mycobacterium sp001665575	82.3331	1054	2060	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	80.969	897	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	80.4659	1028	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_010726645.1	s__Mycobacterium duvalii	80.4082	939	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011620645.1	s__Mycobacterium sp011620645	79.8569	664	2060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004762045.1	s__Mycobacterium sp004762045	79.8442	939	2060	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 18:54:10,393] [INFO] GTDB search result was written to GCF_016313185.1_ASM1631318v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:10,394] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:10,396] [INFO] DFAST_QC result json was written to GCF_016313185.1_ASM1631318v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:10,397] [INFO] DFAST_QC completed!
[2024-01-25 18:54:10,397] [INFO] Total running time: 0h2m20s