[2024-01-25 18:08:35,502] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:35,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:35,504] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c89f593-a585-4717-baa3-804795edf75f/dqc_reference
[2024-01-25 18:08:36,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:36,673] [INFO] Task started: Prodigal
[2024-01-25 18:08:36,673] [INFO] Running command: gunzip -c /var/lib/cwl/stg869a023e-9b69-4c30-a2f1-e87a9c0abd3f/GCF_023516435.1_ASM2351643v1_genomic.fna.gz | prodigal -d GCF_023516435.1_ASM2351643v1_genomic.fna/cds.fna -a GCF_023516435.1_ASM2351643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:47,593] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:47,593] [INFO] Task started: HMMsearch
[2024-01-25 18:08:47,594] [INFO] Running command: hmmsearch --tblout GCF_023516435.1_ASM2351643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c89f593-a585-4717-baa3-804795edf75f/dqc_reference/reference_markers.hmm GCF_023516435.1_ASM2351643v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:47,792] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:47,793] [INFO] Found 6/6 markers.
[2024-01-25 18:08:47,826] [INFO] Query marker FASTA was written to GCF_023516435.1_ASM2351643v1_genomic.fna/markers.fasta
[2024-01-25 18:08:47,826] [INFO] Task started: Blastn
[2024-01-25 18:08:47,827] [INFO] Running command: blastn -query GCF_023516435.1_ASM2351643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c89f593-a585-4717-baa3-804795edf75f/dqc_reference/reference_markers.fasta -out GCF_023516435.1_ASM2351643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:48,843] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:48,845] [INFO] Selected 23 target genomes.
[2024-01-25 18:08:48,846] [INFO] Target genome list was writen to GCF_023516435.1_ASM2351643v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:48,868] [INFO] Task started: fastANI
[2024-01-25 18:08:48,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg869a023e-9b69-4c30-a2f1-e87a9c0abd3f/GCF_023516435.1_ASM2351643v1_genomic.fna.gz --refList GCF_023516435.1_ASM2351643v1_genomic.fna/target_genomes.txt --output GCF_023516435.1_ASM2351643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:13,834] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:13,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c89f593-a585-4717-baa3-804795edf75f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:13,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c89f593-a585-4717-baa3-804795edf75f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:13,848] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:13,848] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:13,849] [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
Jatrophihabitans telluris	strain=N237	GCA_023516435.1	2038343	2038343	type	True	100.0	1397	1397	95	conclusive
Jatrophihabitans endophyticus	strain=DSM 45627	GCA_900129455.1	1206085	1206085	type	True	77.7884	383	1397	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	76.9685	285	1397	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	76.8497	291	1397	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	76.844	256	1397	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	76.7304	288	1397	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	76.6866	255	1397	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	76.68	338	1397	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	76.5861	256	1397	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	76.5633	259	1397	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	76.5569	306	1397	95	below_threshold
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	76.507	253	1397	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	76.483	234	1397	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	76.4753	322	1397	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	76.4379	280	1397	95	below_threshold
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	76.3861	254	1397	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	76.3704	267	1397	95	below_threshold
Actinopolymorpha cephalotaxi	strain=DSM 45117	GCA_013408535.1	504797	504797	type	True	76.3445	238	1397	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	76.173	245	1397	95	below_threshold
Actinoplanes consettensis	strain=NBRC 14913	GCA_018332715.1	113560	113560	type	True	76.1481	283	1397	95	below_threshold
Actinoplanes humidus	strain=NBRC 14915	GCA_016862215.1	113566	113566	type	True	76.1461	257	1397	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	76.1175	263	1397	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	76.1037	248	1397	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:13,850] [INFO] DFAST Taxonomy check result was written to GCF_023516435.1_ASM2351643v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:13,851] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:13,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:13,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c89f593-a585-4717-baa3-804795edf75f/dqc_reference/checkm_data
[2024-01-25 18:09:13,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:13,892] [INFO] Task started: CheckM
[2024-01-25 18:09:13,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023516435.1_ASM2351643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023516435.1_ASM2351643v1_genomic.fna/checkm_input GCF_023516435.1_ASM2351643v1_genomic.fna/checkm_result
[2024-01-25 18:09:52,896] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:52,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:52,914] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:52,914] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:52,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023516435.1_ASM2351643v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:52,915] [INFO] Task started: Blastn
[2024-01-25 18:09:52,915] [INFO] Running command: blastn -query GCF_023516435.1_ASM2351643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c89f593-a585-4717-baa3-804795edf75f/dqc_reference/reference_markers_gtdb.fasta -out GCF_023516435.1_ASM2351643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:54,484] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:54,487] [INFO] Selected 26 target genomes.
[2024-01-25 18:09:54,487] [INFO] Target genome list was writen to GCF_023516435.1_ASM2351643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:54,513] [INFO] Task started: fastANI
[2024-01-25 18:09:54,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg869a023e-9b69-4c30-a2f1-e87a9c0abd3f/GCF_023516435.1_ASM2351643v1_genomic.fna.gz --refList GCF_023516435.1_ASM2351643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023516435.1_ASM2351643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:19,722] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:19,737] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:10:19,737] [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_000421445.1	s__Iso899 sp000421445	77.9449	283	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__Iso899	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129455.1	s__Jatrophihabitans endophyticus	77.7983	382	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__Jatrophihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230215.1	s__MT45 sp900230215	77.6104	302	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__MT45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900100325.1	s__MT45 sp900100325	77.5756	298	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__MT45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299665.1	s__FW021-bin43 sp004299665	77.3932	194	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__FW021-bin43	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241805.1	s__JAFAWL01 sp019241805	77.1083	177	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__JAFAWL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009780925.1	s__WQZC01 sp009780925	77.0525	158	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__WQZC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124835.1	s__Blastococcus xanthinilyticus	76.8267	258	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739085.1	s__Amycolatopsis methanolica	76.649	256	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_003579925.1	s__Jiangella rhizosphaerae	76.5773	257	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105925.1	s__Jiangella alkaliphila	76.5425	308	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007828865.1	s__Kribbella amoyensis	76.4984	254	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024385.1	s__Thermomonospora curvata	76.4901	233	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	99.63	99.63	0.99	0.99	2	-
GCF_011947195.1	s__Planosporangium thailandense	76.486	275	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006912135.1	s__Cryptosporangium phraense	76.4799	322	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473265.1	s__Amycolatopsis thermoflava	76.4568	283	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	98.72	98.72	0.92	0.92	2	-
GCF_003427025.1	s__Jiangella endophytica	76.4391	280	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349105.1	s__Jiangella aurantiaca	76.3733	257	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653695.1	s__Lentzea cavernae	76.3624	264	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408535.1	s__Actinopolymorpha cephalotaxi	76.352	237	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016464705.1	s__Saccharomonospora sp016464705	76.3381	236	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862215.1	s__Actinoplanes humidus	76.1577	254	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901521055.1	s__Cellulomonas hominis_C	76.1564	184	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332715.1	s__Actinoplanes consettensis	76.142	284	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	76.1104	247	1397	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007679345.1	s__Cellulomonas cellulans_A	76.1049	220	1397	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 18:10:19,738] [INFO] GTDB search result was written to GCF_023516435.1_ASM2351643v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:19,739] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:19,743] [INFO] DFAST_QC result json was written to GCF_023516435.1_ASM2351643v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:19,743] [INFO] DFAST_QC completed!
[2024-01-25 18:10:19,743] [INFO] Total running time: 0h1m44s