[2024-01-25 18:14:05,808] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,809] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg2561f164-8c82-4f0d-83ce-a2f240835287/dqc_reference
[2024-01-25 18:14:06,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:06,989] [INFO] Task started: Prodigal
[2024-01-25 18:14:06,989] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc4a907e-db07-420f-9f4d-4ae621923704/GCF_014205115.1_ASM1420511v1_genomic.fna.gz | prodigal -d GCF_014205115.1_ASM1420511v1_genomic.fna/cds.fna -a GCF_014205115.1_ASM1420511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:14,189] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:14,189] [INFO] Task started: HMMsearch
[2024-01-25 18:14:14,189] [INFO] Running command: hmmsearch --tblout GCF_014205115.1_ASM1420511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2561f164-8c82-4f0d-83ce-a2f240835287/dqc_reference/reference_markers.hmm GCF_014205115.1_ASM1420511v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:14,389] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:14,390] [INFO] Found 6/6 markers.
[2024-01-25 18:14:14,412] [INFO] Query marker FASTA was written to GCF_014205115.1_ASM1420511v1_genomic.fna/markers.fasta
[2024-01-25 18:14:14,412] [INFO] Task started: Blastn
[2024-01-25 18:14:14,413] [INFO] Running command: blastn -query GCF_014205115.1_ASM1420511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2561f164-8c82-4f0d-83ce-a2f240835287/dqc_reference/reference_markers.fasta -out GCF_014205115.1_ASM1420511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:15,619] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:15,621] [INFO] Selected 9 target genomes.
[2024-01-25 18:14:15,622] [INFO] Target genome list was writen to GCF_014205115.1_ASM1420511v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:15,627] [INFO] Task started: fastANI
[2024-01-25 18:14:15,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc4a907e-db07-420f-9f4d-4ae621923704/GCF_014205115.1_ASM1420511v1_genomic.fna.gz --refList GCF_014205115.1_ASM1420511v1_genomic.fna/target_genomes.txt --output GCF_014205115.1_ASM1420511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:21,145] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:21,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2561f164-8c82-4f0d-83ce-a2f240835287/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:21,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2561f164-8c82-4f0d-83ce-a2f240835287/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:21,153] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:14:21,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:21,154] [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 endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	100.0	903	903	95	conclusive
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	89.3895	524	903	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_008868275.1	1270	1270	type	True	89.1928	600	903	95	below_threshold
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	89.0741	690	903	95	below_threshold
Micrococcus luteus	strain=NCTC 2665	GCA_000023205.1	1270	1270	type	True	89.0116	706	903	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	85.1743	639	903	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.0662	256	903	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.8829	242	903	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.1133	270	903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:21,156] [INFO] DFAST Taxonomy check result was written to GCF_014205115.1_ASM1420511v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:21,157] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:21,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:21,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2561f164-8c82-4f0d-83ce-a2f240835287/dqc_reference/checkm_data
[2024-01-25 18:14:21,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:21,190] [INFO] Task started: CheckM
[2024-01-25 18:14:21,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205115.1_ASM1420511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205115.1_ASM1420511v1_genomic.fna/checkm_input GCF_014205115.1_ASM1420511v1_genomic.fna/checkm_result
[2024-01-25 18:15:15,817] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:15,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:15,835] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:15,835] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:15,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205115.1_ASM1420511v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:15,836] [INFO] Task started: Blastn
[2024-01-25 18:15:15,836] [INFO] Running command: blastn -query GCF_014205115.1_ASM1420511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2561f164-8c82-4f0d-83ce-a2f240835287/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205115.1_ASM1420511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:17,800] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:17,803] [INFO] Selected 8 target genomes.
[2024-01-25 18:15:17,803] [INFO] Target genome list was writen to GCF_014205115.1_ASM1420511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:17,813] [INFO] Task started: fastANI
[2024-01-25 18:15:17,813] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc4a907e-db07-420f-9f4d-4ae621923704/GCF_014205115.1_ASM1420511v1_genomic.fna.gz --refList GCF_014205115.1_ASM1420511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205115.1_ASM1420511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:23,509] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:23,515] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:23,515] [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_014205115.1	s__Micrococcus endophyticus	100.0	903	903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.47	97.28	0.90	0.88	4	conclusive
GCF_000023205.1	s__Micrococcus luteus	88.974	708	903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.15	95.98	0.88	0.78	124	-
GCF_014204815.1	s__Micrococcus flavus	85.1849	655	903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001570885.1	s__Micrococcus lylae	83.1379	565	903	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	81.3375	495	903	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	80.9756	532	903	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	80.5981	468	903	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	80.2561	474	903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	96.24	96.24	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:23,516] [INFO] GTDB search result was written to GCF_014205115.1_ASM1420511v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:23,517] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:23,530] [INFO] DFAST_QC result json was written to GCF_014205115.1_ASM1420511v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:23,531] [INFO] DFAST_QC completed!
[2024-01-25 18:15:23,531] [INFO] Total running time: 0h1m18s