[2024-01-24 13:40:44,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,386] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg89d6d61b-432f-4c0e-a273-35845a17efc2/dqc_reference
[2024-01-24 13:40:45,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,817] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgc80c98ed-03e0-48b5-b05e-f2fca885c327/GCF_003344865.1_ASM334486v1_genomic.fna.gz | prodigal -d GCF_003344865.1_ASM334486v1_genomic.fna/cds.fna -a GCF_003344865.1_ASM334486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:05,928] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:05,929] [INFO] Task started: HMMsearch
[2024-01-24 13:41:05,929] [INFO] Running command: hmmsearch --tblout GCF_003344865.1_ASM334486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89d6d61b-432f-4c0e-a273-35845a17efc2/dqc_reference/reference_markers.hmm GCF_003344865.1_ASM334486v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:06,280] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:06,281] [INFO] Found 6/6 markers.
[2024-01-24 13:41:06,335] [INFO] Query marker FASTA was written to GCF_003344865.1_ASM334486v1_genomic.fna/markers.fasta
[2024-01-24 13:41:06,335] [INFO] Task started: Blastn
[2024-01-24 13:41:06,335] [INFO] Running command: blastn -query GCF_003344865.1_ASM334486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89d6d61b-432f-4c0e-a273-35845a17efc2/dqc_reference/reference_markers.fasta -out GCF_003344865.1_ASM334486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:07,521] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:07,524] [INFO] Selected 24 target genomes.
[2024-01-24 13:41:07,525] [INFO] Target genome list was writen to GCF_003344865.1_ASM334486v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:07,563] [INFO] Task started: fastANI
[2024-01-24 13:41:07,563] [INFO] Running command: fastANI --query /var/lib/cwl/stgc80c98ed-03e0-48b5-b05e-f2fca885c327/GCF_003344865.1_ASM334486v1_genomic.fna.gz --refList GCF_003344865.1_ASM334486v1_genomic.fna/target_genomes.txt --output GCF_003344865.1_ASM334486v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:28,823] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:28,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89d6d61b-432f-4c0e-a273-35845a17efc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:28,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89d6d61b-432f-4c0e-a273-35845a17efc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:28,842] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:28,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:28,843] [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
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	100.0	2122	2123	95	conclusive
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	88.5358	1559	2123	95	below_threshold
Euzebya tangerina	strain=F10	GCA_003074135.1	591198	591198	type	True	78.1397	545	2123	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	76.1825	313	2123	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	76.0871	317	2123	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	76.0307	331	2123	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	75.9139	366	2123	95	below_threshold
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	75.8304	273	2123	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	75.7801	248	2123	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	75.6401	301	2123	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	75.6066	164	2123	95	below_threshold
Mumia flava	strain=DSM 27763	GCA_002797495.1	1348852	1348852	type	True	75.5042	266	2123	95	below_threshold
Pseudonocardia abyssalis	strain=KRD168	GCA_019263705.2	2792008	2792008	type	True	75.5	372	2123	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	75.4378	182	2123	95	below_threshold
Brachybacterium halotolerans	strain=MASK1Z-5	GCA_016623465.1	2795215	2795215	type	True	75.3559	170	2123	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	75.3516	314	2123	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	75.3133	274	2123	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	75.3058	343	2123	95	below_threshold
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	75.2893	296	2123	95	below_threshold
Streptomyces lonarensis	strain=NCL716	GCA_012033735.1	700599	700599	type	True	75.27	273	2123	95	below_threshold
Labedella gwakjiensis	strain=DSM 21548	GCA_003014675.1	390269	390269	type	True	75.2613	131	2123	95	below_threshold
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	75.2385	131	2123	95	below_threshold
Cellulomonas marina	strain=CGMCC 4.6945	GCA_900111925.1	988821	988821	type	True	75.1567	246	2123	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	75.1557	218	2123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:28,848] [INFO] DFAST Taxonomy check result was written to GCF_003344865.1_ASM334486v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:28,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:28,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:28,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89d6d61b-432f-4c0e-a273-35845a17efc2/dqc_reference/checkm_data
[2024-01-24 13:41:28,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:28,914] [INFO] Task started: CheckM
[2024-01-24 13:41:28,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003344865.1_ASM334486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003344865.1_ASM334486v1_genomic.fna/checkm_input GCF_003344865.1_ASM334486v1_genomic.fna/checkm_result
[2024-01-24 13:44:09,614] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:09,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:09,639] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:09,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:09,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003344865.1_ASM334486v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:09,640] [INFO] Task started: Blastn
[2024-01-24 13:44:09,641] [INFO] Running command: blastn -query GCF_003344865.1_ASM334486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89d6d61b-432f-4c0e-a273-35845a17efc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003344865.1_ASM334486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:11,294] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:11,299] [INFO] Selected 21 target genomes.
[2024-01-24 13:44:11,299] [INFO] Target genome list was writen to GCF_003344865.1_ASM334486v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:11,451] [INFO] Task started: fastANI
[2024-01-24 13:44:11,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgc80c98ed-03e0-48b5-b05e-f2fca885c327/GCF_003344865.1_ASM334486v1_genomic.fna.gz --refList GCF_003344865.1_ASM334486v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003344865.1_ASM334486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:27,425] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:27,446] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:27,447] [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_003344865.1	s__Euzebya sp003344865	100.0	2122	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003073135.1	s__Euzebya rosea	88.536	1559	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003074135.1	s__Euzebya tangerina	78.1491	543	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696915.1	s__JACCXR01 sp013696915	76.5149	287	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__JACCXR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553795.1	s__T1Sed10-49 sp003553795	76.3509	330	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	99.28	99.23	0.95	0.92	4	-
GCA_003021615.1	s__QS-5-72-10 sp003021615	76.2213	159	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__QS-5-72-10	95.0	97.51	97.51	0.71	0.71	2	-
GCF_004300825.1	s__Egicoccus halophilus	76.1636	317	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Egicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007119305.1	s__SKPY01 sp007119305	76.1268	223	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SKPY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133145.1	s__T1Sed10-49 sp007133145	75.8447	220	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	98.98	98.60	0.85	0.78	3	-
GCA_009699265.1	s__Nocardioides sp009699265	75.8384	287	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004322855.1	s__Egibacter rhizosphaerae	75.8287	273	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__Egibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	75.7809	248	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212315.1	s__Nocardioides luti	75.6732	293	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121975.1	s__SKJO01 sp007121975	75.6526	173	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	75.6004	165	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361955.1	s__JABFXA01 sp013361955	75.5365	278	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCF_016623465.1	s__Brachybacterium halotolerans	75.3611	169	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751265.1	s__Pseudokineococcus lusitanus	75.3541	313	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014675.1	s__Labedella gwakjiensis	75.2623	131	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003347015.1	s__Brachybacterium sp003347015	75.2334	193	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002931555.1	s__Pseudoclavibacter sp002931555	75.174	116	2123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	98.27	98.05	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:27,448] [INFO] GTDB search result was written to GCF_003344865.1_ASM334486v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:27,449] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:27,454] [INFO] DFAST_QC result json was written to GCF_003344865.1_ASM334486v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:27,455] [INFO] DFAST_QC completed!
[2024-01-24 13:44:27,455] [INFO] Total running time: 0h3m43s