[2024-01-24 12:31:51,296] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg44bb7dd6-a992-4205-9f1f-1b576c01222f/dqc_reference
[2024-01-24 12:31:52,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,563] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg11cc547d-7e36-4b45-b9ba-e8831967b1a5/GCF_020097155.1_ASM2009715v1_genomic.fna.gz | prodigal -d GCF_020097155.1_ASM2009715v1_genomic.fna/cds.fna -a GCF_020097155.1_ASM2009715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:00,322] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:00,323] [INFO] Task started: HMMsearch
[2024-01-24 12:32:00,323] [INFO] Running command: hmmsearch --tblout GCF_020097155.1_ASM2009715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44bb7dd6-a992-4205-9f1f-1b576c01222f/dqc_reference/reference_markers.hmm GCF_020097155.1_ASM2009715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:00,571] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:00,573] [INFO] Found 6/6 markers.
[2024-01-24 12:32:00,602] [INFO] Query marker FASTA was written to GCF_020097155.1_ASM2009715v1_genomic.fna/markers.fasta
[2024-01-24 12:32:00,603] [INFO] Task started: Blastn
[2024-01-24 12:32:00,603] [INFO] Running command: blastn -query GCF_020097155.1_ASM2009715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44bb7dd6-a992-4205-9f1f-1b576c01222f/dqc_reference/reference_markers.fasta -out GCF_020097155.1_ASM2009715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:01,845] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:01,849] [INFO] Selected 12 target genomes.
[2024-01-24 12:32:01,849] [INFO] Target genome list was writen to GCF_020097155.1_ASM2009715v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:01,855] [INFO] Task started: fastANI
[2024-01-24 12:32:01,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg11cc547d-7e36-4b45-b9ba-e8831967b1a5/GCF_020097155.1_ASM2009715v1_genomic.fna.gz --refList GCF_020097155.1_ASM2009715v1_genomic.fna/target_genomes.txt --output GCF_020097155.1_ASM2009715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:08,986] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:08,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44bb7dd6-a992-4205-9f1f-1b576c01222f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:08,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44bb7dd6-a992-4205-9f1f-1b576c01222f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:08,997] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:32:08,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:32:08,997] [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
Micrococcus luteus	strain=ATCC 4698	GCA_008868275.1	1270	1270	type	True	85.7887	536	882	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	85.6949	487	882	95	below_threshold
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	85.5384	626	882	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_014204815.1	384602	384602	type	True	85.4564	663	882	95	below_threshold
Micrococcus luteus	strain=NCTC 2665	GCA_000023205.1	1270	1270	type	True	85.4283	625	882	95	below_threshold
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	85.4274	662	882	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	85.4082	655	882	95	below_threshold
Micrococcus flavus	strain=CGMCC 1.5361	GCA_014644875.1	384602	384602	type	True	85.2679	660	882	95	below_threshold
Micrococcus lylae	strain=NBRC 15355	GCA_001570885.1	1273	1273	type	True	82.7289	534	882	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.16	250	882	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	76.9835	256	882	95	below_threshold
Quadrisphaera setariae	strain=DD2A	GCA_008041935.1	2593304	2593304	type	True	76.964	285	882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:09,000] [INFO] DFAST Taxonomy check result was written to GCF_020097155.1_ASM2009715v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:09,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:09,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:09,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44bb7dd6-a992-4205-9f1f-1b576c01222f/dqc_reference/checkm_data
[2024-01-24 12:32:09,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:09,035] [INFO] Task started: CheckM
[2024-01-24 12:32:09,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020097155.1_ASM2009715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020097155.1_ASM2009715v1_genomic.fna/checkm_input GCF_020097155.1_ASM2009715v1_genomic.fna/checkm_result
[2024-01-24 12:33:02,030] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:02,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:02,056] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:02,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:02,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020097155.1_ASM2009715v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:02,057] [INFO] Task started: Blastn
[2024-01-24 12:33:02,058] [INFO] Running command: blastn -query GCF_020097155.1_ASM2009715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44bb7dd6-a992-4205-9f1f-1b576c01222f/dqc_reference/reference_markers_gtdb.fasta -out GCF_020097155.1_ASM2009715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:03,950] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:03,954] [INFO] Selected 9 target genomes.
[2024-01-24 12:33:03,955] [INFO] Target genome list was writen to GCF_020097155.1_ASM2009715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:03,965] [INFO] Task started: fastANI
[2024-01-24 12:33:03,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg11cc547d-7e36-4b45-b9ba-e8831967b1a5/GCF_020097155.1_ASM2009715v1_genomic.fna.gz --refList GCF_020097155.1_ASM2009715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020097155.1_ASM2009715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:09,885] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:09,903] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:33:09,903] [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_014204815.1	s__Micrococcus flavus	85.4732	662	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000023205.1	s__Micrococcus luteus	85.4211	625	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.15	95.98	0.88	0.78	124	-
GCF_014205115.1	s__Micrococcus endophyticus	85.3779	663	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.47	97.28	0.90	0.88	4	-
GCF_001570885.1	s__Micrococcus lylae	82.7415	532	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	98.72	97.35	0.93	0.90	6	-
GCF_014205175.1	s__Micrococcus cohnii	81.6429	453	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.00	98.97	0.96	0.96	3	-
GCF_005877055.1	s__Citricoccus sp005877055	80.6286	472	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116905.1	s__Citricoccus terreus	80.5849	419	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224415.1	s__Citricoccus sp000224415	80.0328	436	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	96.24	96.24	0.87	0.87	2	-
GCF_003386075.1	s__Citricoccus muralis	79.583	391	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:09,905] [INFO] GTDB search result was written to GCF_020097155.1_ASM2009715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:09,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:09,910] [INFO] DFAST_QC result json was written to GCF_020097155.1_ASM2009715v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:09,911] [INFO] DFAST_QC completed!
[2024-01-24 12:33:09,911] [INFO] Total running time: 0h1m19s