[2023-06-28 18:27:19,430] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:27:19,433] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:27:19,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg227967d1-3628-45ff-b779-876aecaae905/dqc_reference
[2023-06-28 18:27:21,805] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:27:21,806] [INFO] Task started: Prodigal
[2023-06-28 18:27:21,806] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7ef5875-f303-45a1-8956-7ad31b44dd96/GCA_005881215.1_ASM588121v1_genomic.fna.gz | prodigal -d GCA_005881215.1_ASM588121v1_genomic.fna/cds.fna -a GCA_005881215.1_ASM588121v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:27:36,940] [INFO] Task succeeded: Prodigal
[2023-06-28 18:27:36,940] [INFO] Task started: HMMsearch
[2023-06-28 18:27:36,941] [INFO] Running command: hmmsearch --tblout GCA_005881215.1_ASM588121v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg227967d1-3628-45ff-b779-876aecaae905/dqc_reference/reference_markers.hmm GCA_005881215.1_ASM588121v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:27:37,177] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:27:37,178] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb7ef5875-f303-45a1-8956-7ad31b44dd96/GCA_005881215.1_ASM588121v1_genomic.fna.gz]
[2023-06-28 18:27:37,207] [INFO] Query marker FASTA was written to GCA_005881215.1_ASM588121v1_genomic.fna/markers.fasta
[2023-06-28 18:27:37,208] [INFO] Task started: Blastn
[2023-06-28 18:27:37,208] [INFO] Running command: blastn -query GCA_005881215.1_ASM588121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg227967d1-3628-45ff-b779-876aecaae905/dqc_reference/reference_markers.fasta -out GCA_005881215.1_ASM588121v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:37,880] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:37,885] [INFO] Selected 17 target genomes.
[2023-06-28 18:27:37,886] [INFO] Target genome list was writen to GCA_005881215.1_ASM588121v1_genomic.fna/target_genomes.txt
[2023-06-28 18:27:37,891] [INFO] Task started: fastANI
[2023-06-28 18:27:37,891] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7ef5875-f303-45a1-8956-7ad31b44dd96/GCA_005881215.1_ASM588121v1_genomic.fna.gz --refList GCA_005881215.1_ASM588121v1_genomic.fna/target_genomes.txt --output GCA_005881215.1_ASM588121v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:27:52,208] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:52,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg227967d1-3628-45ff-b779-876aecaae905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:27:52,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg227967d1-3628-45ff-b779-876aecaae905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:27:52,221] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:27:52,221] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:27:52,221] [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
Frankia alni	strain=ACN14a	GCA_000058485.1	1859	1859	type	True	74.979	70	808	95	below_threshold
Nonomuraea endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	74.9147	104	808	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	74.908	63	808	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	74.8319	52	808	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	74.8146	62	808	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	74.73	50	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:27:52,224] [INFO] DFAST Taxonomy check result was written to GCA_005881215.1_ASM588121v1_genomic.fna/tc_result.tsv
[2023-06-28 18:27:52,224] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:27:52,225] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:27:52,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg227967d1-3628-45ff-b779-876aecaae905/dqc_reference/checkm_data
[2023-06-28 18:27:52,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:27:52,257] [INFO] Task started: CheckM
[2023-06-28 18:27:52,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005881215.1_ASM588121v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005881215.1_ASM588121v1_genomic.fna/checkm_input GCA_005881215.1_ASM588121v1_genomic.fna/checkm_result
[2023-06-28 18:28:35,295] [INFO] Task succeeded: CheckM
[2023-06-28 18:28:35,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:28:35,318] [INFO] ===== Completeness check finished =====
[2023-06-28 18:28:35,318] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:28:35,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005881215.1_ASM588121v1_genomic.fna/markers.fasta)
[2023-06-28 18:28:35,319] [INFO] Task started: Blastn
[2023-06-28 18:28:35,319] [INFO] Running command: blastn -query GCA_005881215.1_ASM588121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg227967d1-3628-45ff-b779-876aecaae905/dqc_reference/reference_markers_gtdb.fasta -out GCA_005881215.1_ASM588121v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:28:36,405] [INFO] Task succeeded: Blastn
[2023-06-28 18:28:36,409] [INFO] Selected 13 target genomes.
[2023-06-28 18:28:36,409] [INFO] Target genome list was writen to GCA_005881215.1_ASM588121v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:28:36,419] [INFO] Task started: fastANI
[2023-06-28 18:28:36,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7ef5875-f303-45a1-8956-7ad31b44dd96/GCA_005881215.1_ASM588121v1_genomic.fna.gz --refList GCA_005881215.1_ASM588121v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005881215.1_ASM588121v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:28:44,715] [INFO] Task succeeded: fastANI
[2023-06-28 18:28:44,735] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:28:44,735] [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
GCA_005881215.1	s__CF-13 sp005881215	100.0	798	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005880875.1	s__CF-13 sp005880875	84.2738	511	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	99.07	99.07	0.87	0.87	2	-
GCA_005889535.1	s__CF-13 sp005889535	80.2641	449	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	99.15	99.15	0.85	0.85	2	-
GCA_005882525.1	s__CF-13 sp005882525	80.0617	398	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	98.44	98.44	0.77	0.77	2	-
GCA_005889285.1	s__CF-13 sp005889285	80.0233	291	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882045.1	s__CF-13 sp005882045	79.9735	455	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005889225.1	s__CF-13 sp005889225	79.9487	439	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005880605.1	s__CF-13 sp005880605	79.8646	368	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	98.62	98.62	0.86	0.86	2	-
GCA_005889395.1	s__CF-13 sp005889395	79.8468	366	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005889345.1	s__CF-13 sp005889345	79.705	419	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881235.1	s__CF-13 sp005881235	79.5434	405	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881175.1	s__CF-13 sp005881175	79.5186	439	808	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__CF-121;f__CF-121;g__CF-13	95.0	95.18	95.18	0.80	0.80	2	-
GCA_016709225.1	s__Ga0077550 sp016709225	75.0294	76	808	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
--------------------------------------------------------------------------------
[2023-06-28 18:28:44,737] [INFO] GTDB search result was written to GCA_005881215.1_ASM588121v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:28:44,738] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:28:44,742] [INFO] DFAST_QC result json was written to GCA_005881215.1_ASM588121v1_genomic.fna/dqc_result.json
[2023-06-28 18:28:44,742] [INFO] DFAST_QC completed!
[2023-06-28 18:28:44,742] [INFO] Total running time: 0h1m25s