[2024-01-24 14:50:04,326] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:04,328] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:04,328] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e205913-3a14-4952-b9b8-6c6e371a330c/dqc_reference
[2024-01-24 14:50:05,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:05,652] [INFO] Task started: Prodigal
[2024-01-24 14:50:05,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg769b40ca-eafe-402b-94b1-423ddaef5624/GCF_004798685.1_ASM479868v1_genomic.fna.gz | prodigal -d GCF_004798685.1_ASM479868v1_genomic.fna/cds.fna -a GCF_004798685.1_ASM479868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:17,330] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:17,330] [INFO] Task started: HMMsearch
[2024-01-24 14:50:17,330] [INFO] Running command: hmmsearch --tblout GCF_004798685.1_ASM479868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e205913-3a14-4952-b9b8-6c6e371a330c/dqc_reference/reference_markers.hmm GCF_004798685.1_ASM479868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:17,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:17,583] [INFO] Found 6/6 markers.
[2024-01-24 14:50:17,617] [INFO] Query marker FASTA was written to GCF_004798685.1_ASM479868v1_genomic.fna/markers.fasta
[2024-01-24 14:50:17,617] [INFO] Task started: Blastn
[2024-01-24 14:50:17,617] [INFO] Running command: blastn -query GCF_004798685.1_ASM479868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e205913-3a14-4952-b9b8-6c6e371a330c/dqc_reference/reference_markers.fasta -out GCF_004798685.1_ASM479868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:18,992] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:18,996] [INFO] Selected 16 target genomes.
[2024-01-24 14:50:18,997] [INFO] Target genome list was writen to GCF_004798685.1_ASM479868v1_genomic.fna/target_genomes.txt
[2024-01-24 14:50:19,001] [INFO] Task started: fastANI
[2024-01-24 14:50:19,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg769b40ca-eafe-402b-94b1-423ddaef5624/GCF_004798685.1_ASM479868v1_genomic.fna.gz --refList GCF_004798685.1_ASM479868v1_genomic.fna/target_genomes.txt --output GCF_004798685.1_ASM479868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:50:34,991] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:34,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e205913-3a14-4952-b9b8-6c6e371a330c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:50:34,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e205913-3a14-4952-b9b8-6c6e371a330c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:50:35,004] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:50:35,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:50:35,005] [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 shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	100.0	1303	1303	95	conclusive
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	85.8752	978	1303	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	83.3178	811	1303	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	82.9742	867	1303	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	82.631	852	1303	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	82.5076	860	1303	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	81.6798	692	1303	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.4336	810	1303	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	81.278	742	1303	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	80.9738	697	1303	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.6749	731	1303	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	80.5643	702	1303	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.4799	676	1303	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.0973	582	1303	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.0565	593	1303	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	78.5133	547	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:50:35,007] [INFO] DFAST Taxonomy check result was written to GCF_004798685.1_ASM479868v1_genomic.fna/tc_result.tsv
[2024-01-24 14:50:35,007] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:50:35,007] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:50:35,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e205913-3a14-4952-b9b8-6c6e371a330c/dqc_reference/checkm_data
[2024-01-24 14:50:35,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:50:35,047] [INFO] Task started: CheckM
[2024-01-24 14:50:35,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004798685.1_ASM479868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004798685.1_ASM479868v1_genomic.fna/checkm_input GCF_004798685.1_ASM479868v1_genomic.fna/checkm_result
[2024-01-24 14:51:58,927] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:58,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:58,946] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:58,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:58,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004798685.1_ASM479868v1_genomic.fna/markers.fasta)
[2024-01-24 14:51:58,947] [INFO] Task started: Blastn
[2024-01-24 14:51:58,947] [INFO] Running command: blastn -query GCF_004798685.1_ASM479868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e205913-3a14-4952-b9b8-6c6e371a330c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004798685.1_ASM479868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:52:01,015] [INFO] Task succeeded: Blastn
[2024-01-24 14:52:01,019] [INFO] Selected 12 target genomes.
[2024-01-24 14:52:01,019] [INFO] Target genome list was writen to GCF_004798685.1_ASM479868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:52:01,057] [INFO] Task started: fastANI
[2024-01-24 14:52:01,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg769b40ca-eafe-402b-94b1-423ddaef5624/GCF_004798685.1_ASM479868v1_genomic.fna.gz --refList GCF_004798685.1_ASM479868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004798685.1_ASM479868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:52:15,278] [INFO] Task succeeded: fastANI
[2024-01-24 14:52:15,289] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:52:15,289] [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_004798685.1	s__Cellulomonas shaoxiangyii	100.0	1303	1303	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_004886325.1	s__Cellulomonas telluris	85.8468	981	1303	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720485.1	s__Cellulomonas sp009720485	85.8073	1005	1303	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	83.3767	805	1303	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	83.2478	795	1303	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	82.9813	866	1303	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	82.4919	823	1303	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386485.1	s__Cellulomonas oligotrophica	82.4886	857	1303	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCA_015234515.1	s__Cellulomonas sp015234515	82.4295	864	1303	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715865.1	s__Cellulomonas sp006715865	82.3935	859	1303	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396155.1	s__Cellulomonas septica	81.9311	516	1303	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	80.8474	734	1303	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 14:52:15,291] [INFO] GTDB search result was written to GCF_004798685.1_ASM479868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:52:15,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:52:15,295] [INFO] DFAST_QC result json was written to GCF_004798685.1_ASM479868v1_genomic.fna/dqc_result.json
[2024-01-24 14:52:15,295] [INFO] DFAST_QC completed!
[2024-01-24 14:52:15,295] [INFO] Total running time: 0h2m11s