[2024-01-24 12:53:39,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:39,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:39,562] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd690ee2-cee9-4aaa-9a8e-8176c5cab13f/dqc_reference
[2024-01-24 12:53:40,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:40,938] [INFO] Task started: Prodigal
[2024-01-24 12:53:40,938] [INFO] Running command: gunzip -c /var/lib/cwl/stg79dca778-f279-4e7b-99ac-30fd0920debd/GCF_000092865.1_ASM9286v1_genomic.fna.gz | prodigal -d GCF_000092865.1_ASM9286v1_genomic.fna/cds.fna -a GCF_000092865.1_ASM9286v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:52,914] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:52,915] [INFO] Task started: HMMsearch
[2024-01-24 12:53:52,915] [INFO] Running command: hmmsearch --tblout GCF_000092865.1_ASM9286v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd690ee2-cee9-4aaa-9a8e-8176c5cab13f/dqc_reference/reference_markers.hmm GCF_000092865.1_ASM9286v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:53,215] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:53,217] [INFO] Found 6/6 markers.
[2024-01-24 12:53:53,257] [INFO] Query marker FASTA was written to GCF_000092865.1_ASM9286v1_genomic.fna/markers.fasta
[2024-01-24 12:53:53,258] [INFO] Task started: Blastn
[2024-01-24 12:53:53,258] [INFO] Running command: blastn -query GCF_000092865.1_ASM9286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd690ee2-cee9-4aaa-9a8e-8176c5cab13f/dqc_reference/reference_markers.fasta -out GCF_000092865.1_ASM9286v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:55,184] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:55,187] [INFO] Selected 15 target genomes.
[2024-01-24 12:53:55,188] [INFO] Target genome list was writen to GCF_000092865.1_ASM9286v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:55,194] [INFO] Task started: fastANI
[2024-01-24 12:53:55,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg79dca778-f279-4e7b-99ac-30fd0920debd/GCF_000092865.1_ASM9286v1_genomic.fna.gz --refList GCF_000092865.1_ASM9286v1_genomic.fna/target_genomes.txt --output GCF_000092865.1_ASM9286v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:12,273] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:12,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd690ee2-cee9-4aaa-9a8e-8176c5cab13f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:12,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd690ee2-cee9-4aaa-9a8e-8176c5cab13f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:12,288] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:12,288] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:12,288] [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
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	100.0	1374	1374	95	conclusive
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	85.5519	1012	1374	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	84.7341	873	1374	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	82.7914	842	1374	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	82.5374	842	1374	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	82.3155	858	1374	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	81.5424	761	1374	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	81.3166	721	1374	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	81.1894	735	1374	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	81.0948	742	1374	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.7061	697	1374	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.5778	674	1374	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	80.2334	748	1374	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.3479	695	1374	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.2108	615	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:12,290] [INFO] DFAST Taxonomy check result was written to GCF_000092865.1_ASM9286v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:12,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:12,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:12,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd690ee2-cee9-4aaa-9a8e-8176c5cab13f/dqc_reference/checkm_data
[2024-01-24 12:54:12,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:12,343] [INFO] Task started: CheckM
[2024-01-24 12:54:12,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092865.1_ASM9286v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092865.1_ASM9286v1_genomic.fna/checkm_input GCF_000092865.1_ASM9286v1_genomic.fna/checkm_result
[2024-01-24 12:55:44,230] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:44,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:44,278] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:44,278] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:44,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092865.1_ASM9286v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:44,279] [INFO] Task started: Blastn
[2024-01-24 12:55:44,279] [INFO] Running command: blastn -query GCF_000092865.1_ASM9286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd690ee2-cee9-4aaa-9a8e-8176c5cab13f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092865.1_ASM9286v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:49,550] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:49,553] [INFO] Selected 11 target genomes.
[2024-01-24 12:55:49,553] [INFO] Target genome list was writen to GCF_000092865.1_ASM9286v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:49,562] [INFO] Task started: fastANI
[2024-01-24 12:55:49,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg79dca778-f279-4e7b-99ac-30fd0920debd/GCF_000092865.1_ASM9286v1_genomic.fna.gz --refList GCF_000092865.1_ASM9286v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092865.1_ASM9286v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:03,588] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:03,656] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:03,656] [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_000092865.1	s__Cellulomonas flavigena	100.0	1374	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014836445.1	s__Cellulomonas sp014836445	85.5611	1011	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018623035.1	s__Cellulomonas sp018623035	85.3235	1006	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.51	99.03	0.98	0.95	3	-
GCF_016862775.1	s__Cellulomonas phragmiteti	85.3124	986	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234515.1	s__Cellulomonas sp015234515	84.9508	1012	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552375.1	s__Cellulomonas iranensis	84.7203	875	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_001462455.1	s__Cellulomonas sp001462455	84.6844	843	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114185.1	s__Cellulomonas sp900114185	84.6833	940	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388445.1	s__Cellulomonas sp018388445	84.6111	956	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCF_006538705.1	s__Cellulomonas uda	81.2772	726	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_003755175.1	s__Cellulomonas sp003755175	80.7404	679	1374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:03,661] [INFO] GTDB search result was written to GCF_000092865.1_ASM9286v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:03,662] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:03,672] [INFO] DFAST_QC result json was written to GCF_000092865.1_ASM9286v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:03,673] [INFO] DFAST_QC completed!
[2024-01-24 12:56:03,673] [INFO] Total running time: 0h2m24s