[2024-01-24 14:19:59,722] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,724] [INFO] DQC Reference Directory: /var/lib/cwl/stgcac9982c-d769-4b1f-aedb-fc992a09c49b/dqc_reference
[2024-01-24 14:20:01,034] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:01,035] [INFO] Task started: Prodigal
[2024-01-24 14:20:01,035] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8bbc363-159b-4b15-9517-82581c8324cc/GCF_004306155.1_ASM430615v1_genomic.fna.gz | prodigal -d GCF_004306155.1_ASM430615v1_genomic.fna/cds.fna -a GCF_004306155.1_ASM430615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:11,721] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:11,721] [INFO] Task started: HMMsearch
[2024-01-24 14:20:11,721] [INFO] Running command: hmmsearch --tblout GCF_004306155.1_ASM430615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcac9982c-d769-4b1f-aedb-fc992a09c49b/dqc_reference/reference_markers.hmm GCF_004306155.1_ASM430615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:12,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:12,076] [INFO] Found 6/6 markers.
[2024-01-24 14:20:12,120] [INFO] Query marker FASTA was written to GCF_004306155.1_ASM430615v1_genomic.fna/markers.fasta
[2024-01-24 14:20:12,121] [INFO] Task started: Blastn
[2024-01-24 14:20:12,121] [INFO] Running command: blastn -query GCF_004306155.1_ASM430615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcac9982c-d769-4b1f-aedb-fc992a09c49b/dqc_reference/reference_markers.fasta -out GCF_004306155.1_ASM430615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:13,551] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:13,555] [INFO] Selected 16 target genomes.
[2024-01-24 14:20:13,556] [INFO] Target genome list was writen to GCF_004306155.1_ASM430615v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:13,611] [INFO] Task started: fastANI
[2024-01-24 14:20:13,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8bbc363-159b-4b15-9517-82581c8324cc/GCF_004306155.1_ASM430615v1_genomic.fna.gz --refList GCF_004306155.1_ASM430615v1_genomic.fna/target_genomes.txt --output GCF_004306155.1_ASM430615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:29,946] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:29,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcac9982c-d769-4b1f-aedb-fc992a09c49b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:29,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcac9982c-d769-4b1f-aedb-fc992a09c49b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:29,966] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:29,966] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:29,967] [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 biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	100.0	1198	1211	95	conclusive
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	86.6853	954	1211	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	86.6777	969	1211	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	82.2885	731	1211	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	82.2395	792	1211	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	82.1171	673	1211	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	82.0226	679	1211	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	81.7628	743	1211	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	81.6428	723	1211	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	81.4609	688	1211	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	81.3619	742	1211	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	81.0816	709	1211	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.8131	679	1211	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.4493	615	1211	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.1944	595	1211	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.1434	574	1211	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:29,969] [INFO] DFAST Taxonomy check result was written to GCF_004306155.1_ASM430615v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:29,970] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:29,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:29,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcac9982c-d769-4b1f-aedb-fc992a09c49b/dqc_reference/checkm_data
[2024-01-24 14:20:29,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:30,012] [INFO] Task started: CheckM
[2024-01-24 14:20:30,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004306155.1_ASM430615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004306155.1_ASM430615v1_genomic.fna/checkm_input GCF_004306155.1_ASM430615v1_genomic.fna/checkm_result
[2024-01-24 14:21:20,030] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:20,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:20,053] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:20,053] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:20,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004306155.1_ASM430615v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:20,054] [INFO] Task started: Blastn
[2024-01-24 14:21:20,054] [INFO] Running command: blastn -query GCF_004306155.1_ASM430615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcac9982c-d769-4b1f-aedb-fc992a09c49b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004306155.1_ASM430615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:22,309] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:22,312] [INFO] Selected 11 target genomes.
[2024-01-24 14:21:22,312] [INFO] Target genome list was writen to GCF_004306155.1_ASM430615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:22,404] [INFO] Task started: fastANI
[2024-01-24 14:21:22,404] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8bbc363-159b-4b15-9517-82581c8324cc/GCF_004306155.1_ASM430615v1_genomic.fna.gz --refList GCF_004306155.1_ASM430615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004306155.1_ASM430615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:34,331] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:34,345] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:34,346] [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_004306155.1	s__Cellulomonas biazotea	100.0	1198	1211	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_012396155.1	s__Cellulomonas septica	87.2337	626	1211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851725.1	s__Cellulomonas algicola	87.1398	872	1211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCF_000212695.1	s__Cellulomonas fimi	86.7095	966	1211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_016862675.1	s__Cellulomonas chitinilytica	83.5019	868	1211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744555.1	s__Cellulomonas sp017744555	83.343	800	1211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001429255.1	s__Cellulomonas sp001429255	82.1108	763	1211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCF_000312005.1	s__Cellulomonas massiliensis	82.0531	678	1211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013409305.1	s__Cellulomonas soli	81.4102	693	1211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114185.1	s__Cellulomonas sp900114185	81.0293	724	1211	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	80.7281	700	1211	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 14:21:34,347] [INFO] GTDB search result was written to GCF_004306155.1_ASM430615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:34,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:34,352] [INFO] DFAST_QC result json was written to GCF_004306155.1_ASM430615v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:34,352] [INFO] DFAST_QC completed!
[2024-01-24 14:21:34,352] [INFO] Total running time: 0h1m35s