[2024-01-25 19:34:50,873] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:50,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:50,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg57ca536c-39f4-4c29-9204-0092576c7279/dqc_reference
[2024-01-25 19:34:51,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:51,980] [INFO] Task started: Prodigal
[2024-01-25 19:34:51,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg25f78927-baa4-4d94-831d-f0724f877935/GCF_016742955.1_ASM1674295v1_genomic.fna.gz | prodigal -d GCF_016742955.1_ASM1674295v1_genomic.fna/cds.fna -a GCF_016742955.1_ASM1674295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:04,271] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:04,271] [INFO] Task started: HMMsearch
[2024-01-25 19:35:04,271] [INFO] Running command: hmmsearch --tblout GCF_016742955.1_ASM1674295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57ca536c-39f4-4c29-9204-0092576c7279/dqc_reference/reference_markers.hmm GCF_016742955.1_ASM1674295v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:04,564] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:04,565] [INFO] Found 6/6 markers.
[2024-01-25 19:35:04,609] [INFO] Query marker FASTA was written to GCF_016742955.1_ASM1674295v1_genomic.fna/markers.fasta
[2024-01-25 19:35:04,609] [INFO] Task started: Blastn
[2024-01-25 19:35:04,609] [INFO] Running command: blastn -query GCF_016742955.1_ASM1674295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57ca536c-39f4-4c29-9204-0092576c7279/dqc_reference/reference_markers.fasta -out GCF_016742955.1_ASM1674295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:05,741] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:05,744] [INFO] Selected 15 target genomes.
[2024-01-25 19:35:05,745] [INFO] Target genome list was writen to GCF_016742955.1_ASM1674295v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:05,749] [INFO] Task started: fastANI
[2024-01-25 19:35:05,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg25f78927-baa4-4d94-831d-f0724f877935/GCF_016742955.1_ASM1674295v1_genomic.fna.gz --refList GCF_016742955.1_ASM1674295v1_genomic.fna/target_genomes.txt --output GCF_016742955.1_ASM1674295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:20,198] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:20,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57ca536c-39f4-4c29-9204-0092576c7279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:20,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57ca536c-39f4-4c29-9204-0092576c7279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:20,208] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:35:20,209] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:20,209] [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
Myceligenerans indicum	strain=I2	GCA_016742955.1	2593663	2593663	type	True	100.0	1610	1616	95	conclusive
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	86.1455	1126	1616	95	below_threshold
Myceligenerans salitolerans	strain=XHU 5031	GCA_017349295.1	1230528	1230528	type	True	85.1532	1096	1616	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	80.0554	728	1616	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	80.0399	819	1616	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	80.0062	742	1616	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	79.9616	763	1616	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	79.7035	756	1616	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	78.5751	515	1616	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.1686	482	1616	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.0755	455	1616	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.0271	439	1616	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	77.8913	447	1616	95	below_threshold
Cellulomonas marina	strain=CGMCC 4.6945	GCA_900111925.1	988821	988821	type	True	77.5881	425	1616	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.5138	477	1616	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:20,210] [INFO] DFAST Taxonomy check result was written to GCF_016742955.1_ASM1674295v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:20,211] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:20,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:20,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57ca536c-39f4-4c29-9204-0092576c7279/dqc_reference/checkm_data
[2024-01-25 19:35:20,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:20,260] [INFO] Task started: CheckM
[2024-01-25 19:35:20,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016742955.1_ASM1674295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016742955.1_ASM1674295v1_genomic.fna/checkm_input GCF_016742955.1_ASM1674295v1_genomic.fna/checkm_result
[2024-01-25 19:36:37,234] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:37,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:37,274] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:37,274] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:37,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016742955.1_ASM1674295v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:37,277] [INFO] Task started: Blastn
[2024-01-25 19:36:37,277] [INFO] Running command: blastn -query GCF_016742955.1_ASM1674295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57ca536c-39f4-4c29-9204-0092576c7279/dqc_reference/reference_markers_gtdb.fasta -out GCF_016742955.1_ASM1674295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:39,021] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:39,025] [INFO] Selected 13 target genomes.
[2024-01-25 19:36:39,025] [INFO] Target genome list was writen to GCF_016742955.1_ASM1674295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:39,035] [INFO] Task started: fastANI
[2024-01-25 19:36:39,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg25f78927-baa4-4d94-831d-f0724f877935/GCF_016742955.1_ASM1674295v1_genomic.fna.gz --refList GCF_016742955.1_ASM1674295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016742955.1_ASM1674295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:53,382] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:53,391] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:53,391] [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_016742955.1	s__Myceligenerans indicum	100.0	1610	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003814695.1	s__Myceligenerans xiligouense	86.1679	1123	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014892515.1	s__Myceligenerans sp014892515	85.8896	1148	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017349295.1	s__Myceligenerans salitolerans	85.1547	1095	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137995.1	s__Promicromonospora sukumoe	80.0804	813	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004695.1	s__Promicromonospora citrea	80.0782	726	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_900608595.1	s__Promicromonospora panici	80.0595	783	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058225.1	s__Promicromonospora sp003058225	80.035	845	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	98.27	98.27	0.94	0.94	2	-
GCF_003550025.1	s__Promicromonospora thailandica	80.0229	811	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750215.1	s__Xylanimonas variabilis_A	79.5524	453	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946865.1	s__Antribacter gilvus	79.4069	691	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Antribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846865.1	s__Xylanimonas puerhi	79.2708	560	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	78.7614	519	1616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:53,392] [INFO] GTDB search result was written to GCF_016742955.1_ASM1674295v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:53,393] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:53,396] [INFO] DFAST_QC result json was written to GCF_016742955.1_ASM1674295v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:53,396] [INFO] DFAST_QC completed!
[2024-01-25 19:36:53,396] [INFO] Total running time: 0h2m3s