[2024-01-25 19:06:35,703] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:35,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:35,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bda7c45-f0d2-4d20-9450-27d1afa39310/dqc_reference
[2024-01-25 19:06:36,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:36,864] [INFO] Task started: Prodigal
[2024-01-25 19:06:36,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg04f52e06-2b79-4358-ae72-215773a14a9c/GCF_001552375.1_ASM155237v1_genomic.fna.gz | prodigal -d GCF_001552375.1_ASM155237v1_genomic.fna/cds.fna -a GCF_001552375.1_ASM155237v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:45,832] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:45,832] [INFO] Task started: HMMsearch
[2024-01-25 19:06:45,832] [INFO] Running command: hmmsearch --tblout GCF_001552375.1_ASM155237v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bda7c45-f0d2-4d20-9450-27d1afa39310/dqc_reference/reference_markers.hmm GCF_001552375.1_ASM155237v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:46,059] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:46,060] [INFO] Found 6/6 markers.
[2024-01-25 19:06:46,093] [INFO] Query marker FASTA was written to GCF_001552375.1_ASM155237v1_genomic.fna/markers.fasta
[2024-01-25 19:06:46,093] [INFO] Task started: Blastn
[2024-01-25 19:06:46,093] [INFO] Running command: blastn -query GCF_001552375.1_ASM155237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bda7c45-f0d2-4d20-9450-27d1afa39310/dqc_reference/reference_markers.fasta -out GCF_001552375.1_ASM155237v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:47,401] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:47,404] [INFO] Selected 15 target genomes.
[2024-01-25 19:06:47,404] [INFO] Target genome list was writen to GCF_001552375.1_ASM155237v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:47,408] [INFO] Task started: fastANI
[2024-01-25 19:06:47,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg04f52e06-2b79-4358-ae72-215773a14a9c/GCF_001552375.1_ASM155237v1_genomic.fna.gz --refList GCF_001552375.1_ASM155237v1_genomic.fna/target_genomes.txt --output GCF_001552375.1_ASM155237v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:03,613] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:03,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bda7c45-f0d2-4d20-9450-27d1afa39310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:03,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bda7c45-f0d2-4d20-9450-27d1afa39310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:03,624] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:07:03,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:03,625] [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 iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	100.0	1214	1221	95	conclusive
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	84.7943	871	1221	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	84.4649	897	1221	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	83.3673	848	1221	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	83.1626	816	1221	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	82.8914	836	1221	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	81.9693	710	1221	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	81.9689	757	1221	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.9142	785	1221	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	81.4791	688	1221	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	81.3127	693	1221	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	81.1741	700	1221	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.6829	689	1221	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.2674	602	1221	95	below_threshold
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	78.7307	458	1221	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:03,626] [INFO] DFAST Taxonomy check result was written to GCF_001552375.1_ASM155237v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:03,627] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:03,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:03,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bda7c45-f0d2-4d20-9450-27d1afa39310/dqc_reference/checkm_data
[2024-01-25 19:07:03,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:03,681] [INFO] Task started: CheckM
[2024-01-25 19:07:03,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552375.1_ASM155237v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552375.1_ASM155237v1_genomic.fna/checkm_input GCF_001552375.1_ASM155237v1_genomic.fna/checkm_result
[2024-01-25 19:07:57,708] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:57,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:57,726] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:57,727] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:57,727] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552375.1_ASM155237v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:57,727] [INFO] Task started: Blastn
[2024-01-25 19:07:57,727] [INFO] Running command: blastn -query GCF_001552375.1_ASM155237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bda7c45-f0d2-4d20-9450-27d1afa39310/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552375.1_ASM155237v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:59,938] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:59,941] [INFO] Selected 13 target genomes.
[2024-01-25 19:07:59,941] [INFO] Target genome list was writen to GCF_001552375.1_ASM155237v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:59,953] [INFO] Task started: fastANI
[2024-01-25 19:07:59,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg04f52e06-2b79-4358-ae72-215773a14a9c/GCF_001552375.1_ASM155237v1_genomic.fna.gz --refList GCF_001552375.1_ASM155237v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552375.1_ASM155237v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:14,666] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:14,674] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:14,675] [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_001552375.1	s__Cellulomonas iranensis	100.0	1214	1221	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	conclusive
GCF_001462455.1	s__Cellulomonas sp001462455	92.6172	982	1221	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	84.8629	866	1221	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836445.1	s__Cellulomonas sp014836445	84.5101	892	1221	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	84.3755	885	1221	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862775.1	s__Cellulomonas phragmiteti	84.3202	889	1221	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	84.186	893	1221	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCA_015234515.1	s__Cellulomonas sp015234515	83.9364	870	1221	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004886325.1	s__Cellulomonas telluris	83.3726	849	1221	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	83.1264	820	1221	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012396155.1	s__Cellulomonas septica	82.3403	490	1221	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	81.383	736	1221	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085345.1	s__Isoptericola sediminis	78.7035	461	1221	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:08:14,676] [INFO] GTDB search result was written to GCF_001552375.1_ASM155237v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:14,677] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:14,679] [INFO] DFAST_QC result json was written to GCF_001552375.1_ASM155237v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:14,680] [INFO] DFAST_QC completed!
[2024-01-25 19:08:14,680] [INFO] Total running time: 0h1m39s