[2024-01-24 14:37:46,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:46,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:46,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg52a8ee2c-da42-4401-87bf-589c31656181/dqc_reference
[2024-01-24 14:37:50,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:50,280] [INFO] Task started: Prodigal
[2024-01-24 14:37:50,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c8a5593-b2ce-4dac-992c-d00826f08467/GCF_014201095.1_ASM1420109v1_genomic.fna.gz | prodigal -d GCF_014201095.1_ASM1420109v1_genomic.fna/cds.fna -a GCF_014201095.1_ASM1420109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:02,759] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:02,759] [INFO] Task started: HMMsearch
[2024-01-24 14:38:02,759] [INFO] Running command: hmmsearch --tblout GCF_014201095.1_ASM1420109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52a8ee2c-da42-4401-87bf-589c31656181/dqc_reference/reference_markers.hmm GCF_014201095.1_ASM1420109v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:03,084] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:03,086] [INFO] Found 6/6 markers.
[2024-01-24 14:38:03,135] [INFO] Query marker FASTA was written to GCF_014201095.1_ASM1420109v1_genomic.fna/markers.fasta
[2024-01-24 14:38:03,135] [INFO] Task started: Blastn
[2024-01-24 14:38:03,135] [INFO] Running command: blastn -query GCF_014201095.1_ASM1420109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52a8ee2c-da42-4401-87bf-589c31656181/dqc_reference/reference_markers.fasta -out GCF_014201095.1_ASM1420109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:04,619] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:04,622] [INFO] Selected 19 target genomes.
[2024-01-24 14:38:04,623] [INFO] Target genome list was writen to GCF_014201095.1_ASM1420109v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:04,629] [INFO] Task started: fastANI
[2024-01-24 14:38:04,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c8a5593-b2ce-4dac-992c-d00826f08467/GCF_014201095.1_ASM1420109v1_genomic.fna.gz --refList GCF_014201095.1_ASM1420109v1_genomic.fna/target_genomes.txt --output GCF_014201095.1_ASM1420109v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:24,359] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:24,359] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52a8ee2c-da42-4401-87bf-589c31656181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:24,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52a8ee2c-da42-4401-87bf-589c31656181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:24,375] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:38:24,375] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:24,375] [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 hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	100.0	1496	1496	95	conclusive
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	99.9124	1379	1496	95	conclusive
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	82.0475	832	1496	95	below_threshold
Cellulomonas taurus	strain=P40-2	GCA_012931845.1	2729175	2729175	type	True	81.7242	755	1496	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	80.7233	756	1496	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	80.6007	759	1496	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.5236	715	1496	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	80.4286	758	1496	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.4098	688	1496	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	80.3789	617	1496	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	80.3474	732	1496	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.3213	677	1496	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	80.2589	674	1496	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	80.137	684	1496	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	80.1186	704	1496	95	below_threshold
Cellulomonas composti	strain=NBRC 100758	GCA_007990245.1	266130	266130	type	True	80.0881	625	1496	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.9793	682	1496	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.9043	574	1496	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.7682	601	1496	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:24,377] [INFO] DFAST Taxonomy check result was written to GCF_014201095.1_ASM1420109v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:24,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:24,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:24,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52a8ee2c-da42-4401-87bf-589c31656181/dqc_reference/checkm_data
[2024-01-24 14:38:24,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:24,424] [INFO] Task started: CheckM
[2024-01-24 14:38:24,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201095.1_ASM1420109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201095.1_ASM1420109v1_genomic.fna/checkm_input GCF_014201095.1_ASM1420109v1_genomic.fna/checkm_result
[2024-01-24 14:39:35,303] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:35,305] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:35,324] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:35,325] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:35,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201095.1_ASM1420109v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:35,325] [INFO] Task started: Blastn
[2024-01-24 14:39:35,326] [INFO] Running command: blastn -query GCF_014201095.1_ASM1420109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52a8ee2c-da42-4401-87bf-589c31656181/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201095.1_ASM1420109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:37,668] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:37,672] [INFO] Selected 8 target genomes.
[2024-01-24 14:39:37,672] [INFO] Target genome list was writen to GCF_014201095.1_ASM1420109v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:37,679] [INFO] Task started: fastANI
[2024-01-24 14:39:37,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c8a5593-b2ce-4dac-992c-d00826f08467/GCF_014201095.1_ASM1420109v1_genomic.fna.gz --refList GCF_014201095.1_ASM1420109v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201095.1_ASM1420109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:48,060] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:48,073] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:48,073] [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_014201095.1	s__Cellulomonas hominis	100.0	1496	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.15	98.63	0.95	0.92	4	conclusive
GCF_011603975.1	s__Cellulomonas sp011603975	86.3451	858	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	86.2248	862	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409475.1	s__Cellulomonas hominis_B	86.0901	1032	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	86.0891	892	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033115.1	s__Cellulomonas sp008033115	86.0003	1042	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_007679345.1	s__Cellulomonas cellulans_A	85.9643	1023	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862755.1	s__Cellulomonas pakistanensis	85.9277	957	1496	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 14:39:48,077] [INFO] GTDB search result was written to GCF_014201095.1_ASM1420109v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:48,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:48,082] [INFO] DFAST_QC result json was written to GCF_014201095.1_ASM1420109v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:48,082] [INFO] DFAST_QC completed!
[2024-01-24 14:39:48,082] [INFO] Total running time: 0h2m1s