[2024-01-25 19:02:50,613] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:50,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:50,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf15c521-32ba-48df-bb6a-4c6cb2e4b1bb/dqc_reference
[2024-01-25 19:02:51,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:51,745] [INFO] Task started: Prodigal
[2024-01-25 19:02:51,746] [INFO] Running command: gunzip -c /var/lib/cwl/stga4733c33-fe96-4f20-a001-eacbc6360f50/GCF_016862775.1_ASM1686277v1_genomic.fna.gz | prodigal -d GCF_016862775.1_ASM1686277v1_genomic.fna/cds.fna -a GCF_016862775.1_ASM1686277v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:01,918] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:01,919] [INFO] Task started: HMMsearch
[2024-01-25 19:03:01,919] [INFO] Running command: hmmsearch --tblout GCF_016862775.1_ASM1686277v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf15c521-32ba-48df-bb6a-4c6cb2e4b1bb/dqc_reference/reference_markers.hmm GCF_016862775.1_ASM1686277v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:02,166] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:02,168] [INFO] Found 6/6 markers.
[2024-01-25 19:03:02,204] [INFO] Query marker FASTA was written to GCF_016862775.1_ASM1686277v1_genomic.fna/markers.fasta
[2024-01-25 19:03:02,204] [INFO] Task started: Blastn
[2024-01-25 19:03:02,204] [INFO] Running command: blastn -query GCF_016862775.1_ASM1686277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf15c521-32ba-48df-bb6a-4c6cb2e4b1bb/dqc_reference/reference_markers.fasta -out GCF_016862775.1_ASM1686277v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:03,440] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:03,442] [INFO] Selected 18 target genomes.
[2024-01-25 19:03:03,443] [INFO] Target genome list was writen to GCF_016862775.1_ASM1686277v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:03,450] [INFO] Task started: fastANI
[2024-01-25 19:03:03,451] [INFO] Running command: fastANI --query /var/lib/cwl/stga4733c33-fe96-4f20-a001-eacbc6360f50/GCF_016862775.1_ASM1686277v1_genomic.fna.gz --refList GCF_016862775.1_ASM1686277v1_genomic.fna/target_genomes.txt --output GCF_016862775.1_ASM1686277v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:21,191] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:21,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf15c521-32ba-48df-bb6a-4c6cb2e4b1bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:21,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf15c521-32ba-48df-bb6a-4c6cb2e4b1bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:21,203] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:03:21,203] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:03:21,204] [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 avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	86.3018	1025	1355	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	85.1676	991	1355	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	84.5666	866	1355	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	82.3774	844	1355	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	82.3593	858	1355	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	81.0773	706	1355	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	80.8393	701	1355	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	80.7537	805	1355	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	80.7289	717	1355	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.6161	763	1355	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	80.4817	728	1355	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	80.4078	741	1355	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.3869	716	1355	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.2465	691	1355	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	79.7838	694	1355	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	79.7785	680	1355	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.1096	673	1355	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.7664	565	1355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:21,206] [INFO] DFAST Taxonomy check result was written to GCF_016862775.1_ASM1686277v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:21,206] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:21,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:21,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf15c521-32ba-48df-bb6a-4c6cb2e4b1bb/dqc_reference/checkm_data
[2024-01-25 19:03:21,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:21,248] [INFO] Task started: CheckM
[2024-01-25 19:03:21,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862775.1_ASM1686277v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862775.1_ASM1686277v1_genomic.fna/checkm_input GCF_016862775.1_ASM1686277v1_genomic.fna/checkm_result
[2024-01-25 19:04:29,679] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:29,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:29,699] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:29,700] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:29,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862775.1_ASM1686277v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:29,701] [INFO] Task started: Blastn
[2024-01-25 19:04:29,701] [INFO] Running command: blastn -query GCF_016862775.1_ASM1686277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf15c521-32ba-48df-bb6a-4c6cb2e4b1bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862775.1_ASM1686277v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:31,719] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:31,722] [INFO] Selected 12 target genomes.
[2024-01-25 19:04:31,722] [INFO] Target genome list was writen to GCF_016862775.1_ASM1686277v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:31,727] [INFO] Task started: fastANI
[2024-01-25 19:04:31,727] [INFO] Running command: fastANI --query /var/lib/cwl/stga4733c33-fe96-4f20-a001-eacbc6360f50/GCF_016862775.1_ASM1686277v1_genomic.fna.gz --refList GCF_016862775.1_ASM1686277v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862775.1_ASM1686277v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:44,776] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:44,785] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:44,785] [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_016862775.1	s__Cellulomonas phragmiteti	100.0	1354	1355	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	86.3126	1025	1355	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	86.0023	984	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.51	99.03	0.98	0.95	3	-
GCA_015234515.1	s__Cellulomonas sp015234515	85.5619	977	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092865.1	s__Cellulomonas flavigena	85.1454	993	1355	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	84.7621	972	1355	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	84.7598	966	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCF_001552375.1	s__Cellulomonas iranensis	84.5669	866	1355	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	84.3863	869	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538705.1	s__Cellulomonas uda	80.815	704	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_007989805.1	s__Cellulomonas xylanilytica	80.4785	728	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	80.4204	740	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:44,786] [INFO] GTDB search result was written to GCF_016862775.1_ASM1686277v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:44,787] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:44,790] [INFO] DFAST_QC result json was written to GCF_016862775.1_ASM1686277v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:44,790] [INFO] DFAST_QC completed!
[2024-01-25 19:04:44,790] [INFO] Total running time: 0h1m54s