[2024-01-24 12:14:48,953] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg7609908a-2e41-4542-8124-c7a4231a1783/dqc_reference
[2024-01-24 12:14:50,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,223] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg2383eaa4-321f-434d-901d-74e5475bf560/GCF_004322855.1_ASM432285v1_genomic.fna.gz | prodigal -d GCF_004322855.1_ASM432285v1_genomic.fna/cds.fna -a GCF_004322855.1_ASM432285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:04,126] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:04,126] [INFO] Task started: HMMsearch
[2024-01-24 12:15:04,127] [INFO] Running command: hmmsearch --tblout GCF_004322855.1_ASM432285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7609908a-2e41-4542-8124-c7a4231a1783/dqc_reference/reference_markers.hmm GCF_004322855.1_ASM432285v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:04,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:04,485] [INFO] Found 6/6 markers.
[2024-01-24 12:15:04,531] [INFO] Query marker FASTA was written to GCF_004322855.1_ASM432285v1_genomic.fna/markers.fasta
[2024-01-24 12:15:04,532] [INFO] Task started: Blastn
[2024-01-24 12:15:04,532] [INFO] Running command: blastn -query GCF_004322855.1_ASM432285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7609908a-2e41-4542-8124-c7a4231a1783/dqc_reference/reference_markers.fasta -out GCF_004322855.1_ASM432285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:05,503] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:05,507] [INFO] Selected 24 target genomes.
[2024-01-24 12:15:05,507] [INFO] Target genome list was writen to GCF_004322855.1_ASM432285v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:05,523] [INFO] Task started: fastANI
[2024-01-24 12:15:05,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg2383eaa4-321f-434d-901d-74e5475bf560/GCF_004322855.1_ASM432285v1_genomic.fna.gz --refList GCF_004322855.1_ASM432285v1_genomic.fna/target_genomes.txt --output GCF_004322855.1_ASM432285v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:28,532] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:28,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7609908a-2e41-4542-8124-c7a4231a1783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:28,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7609908a-2e41-4542-8124-c7a4231a1783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:28,554] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:28,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:28,554] [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
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	100.0	1545	1545	95	conclusive
Euzebya tangerina	strain=F10	GCA_003074135.1	591198	591198	type	True	76.2392	144	1545	95	below_threshold
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	76.1415	265	1545	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.9791	263	1545	95	below_threshold
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	75.9597	272	1545	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	75.8236	280	1545	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	75.6759	205	1545	95	below_threshold
Gephyromycinifex aptenodytis	strain=NJES-13	GCA_012277275.1	2716227	2716227	type	True	75.5194	80	1545	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	75.2615	287	1545	95	below_threshold
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	75.2458	219	1545	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	75.2187	116	1545	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	75.2133	167	1545	95	below_threshold
Jatrophihabitans endophyticus	strain=DSM 45627	GCA_900129455.1	1206085	1206085	type	True	75.1986	250	1545	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	75.1689	245	1545	95	below_threshold
Nocardioides aromaticivorans	strain=DSM 15131	GCA_013408525.1	200618	200618	type	True	75.1135	255	1545	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	75.076	262	1545	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	75.0642	315	1545	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	75.0503	274	1545	95	below_threshold
Halorubrum salinum	strain=GX71	GCA_024494575.1	767517	767517	type	True	74.7492	86	1545	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.7335	282	1545	95	below_threshold
Halolamina rubra	strain=CBA1107	GCA_000739555.1	1380430	1380430	type	True	74.6817	120	1545	95	below_threshold
Halarchaeum grantii	strain=JCM 19585	GCA_014647455.2	1193105	1193105	type	True	74.6664	124	1545	95	below_threshold
Halolamina pelagica	strain=CGMCC 1.10329	GCA_900115675.1	699431	699431	type	True	74.6322	100	1545	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,556] [INFO] DFAST Taxonomy check result was written to GCF_004322855.1_ASM432285v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:28,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:28,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:28,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7609908a-2e41-4542-8124-c7a4231a1783/dqc_reference/checkm_data
[2024-01-24 12:15:28,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:28,604] [INFO] Task started: CheckM
[2024-01-24 12:15:28,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004322855.1_ASM432285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004322855.1_ASM432285v1_genomic.fna/checkm_input GCF_004322855.1_ASM432285v1_genomic.fna/checkm_result
[2024-01-24 12:16:18,516] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:18,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:18,537] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:18,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:18,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004322855.1_ASM432285v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:18,538] [INFO] Task started: Blastn
[2024-01-24 12:16:18,539] [INFO] Running command: blastn -query GCF_004322855.1_ASM432285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7609908a-2e41-4542-8124-c7a4231a1783/dqc_reference/reference_markers_gtdb.fasta -out GCF_004322855.1_ASM432285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:20,096] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:20,101] [INFO] Selected 13 target genomes.
[2024-01-24 12:16:20,102] [INFO] Target genome list was writen to GCF_004322855.1_ASM432285v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:20,112] [INFO] Task started: fastANI
[2024-01-24 12:16:20,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg2383eaa4-321f-434d-901d-74e5475bf560/GCF_004322855.1_ASM432285v1_genomic.fna.gz --refList GCF_004322855.1_ASM432285v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004322855.1_ASM432285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:29,502] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:29,517] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:29,517] [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_004322855.1	s__Egibacter rhizosphaerae	100.0	1545	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__Egibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003553795.1	s__T1Sed10-49 sp003553795	77.8592	435	1545	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_007126835.1	s__SLAO01 sp007126835	77.4872	213	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SLAO01	95.0	98.77	98.77	0.62	0.62	2	-
GCA_007119035.1	s__SKQL01 sp007119035	77.3263	195	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SKQL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133145.1	s__T1Sed10-49 sp007133145	77.2659	278	1545	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_007119305.1	s__SKPY01 sp007119305	76.7214	254	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SKPY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696915.1	s__JACCXR01 sp013696915	76.7019	272	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__JACCXR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379795.1	s__WHTC01 sp009379795	76.6974	177	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__WHTC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377835.1	s__WHTG01 sp009377835	76.2502	148	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__WHTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073135.1	s__Euzebya rosea	76.1096	266	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344865.1	s__Euzebya sp003344865	75.9465	276	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642295.1	s__Streptomyces venezuelae_C	75.1954	172	1545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:29,519] [INFO] GTDB search result was written to GCF_004322855.1_ASM432285v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:29,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:29,524] [INFO] DFAST_QC result json was written to GCF_004322855.1_ASM432285v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:29,524] [INFO] DFAST_QC completed!
[2024-01-24 12:16:29,524] [INFO] Total running time: 0h1m41s