[2023-06-30 12:00:37,769] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:00:37,771] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:00:37,771] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9e4bbde-67e5-4579-b883-bff8e4bea608/dqc_reference
[2023-06-30 12:00:39,013] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:00:39,014] [INFO] Task started: Prodigal
[2023-06-30 12:00:39,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg41279617-2050-47ac-bf5e-8903e415997c/GCA_024653385.1_ASM2465338v1_genomic.fna.gz | prodigal -d GCA_024653385.1_ASM2465338v1_genomic.fna/cds.fna -a GCA_024653385.1_ASM2465338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:00:55,591] [INFO] Task succeeded: Prodigal
[2023-06-30 12:00:55,592] [INFO] Task started: HMMsearch
[2023-06-30 12:00:55,592] [INFO] Running command: hmmsearch --tblout GCA_024653385.1_ASM2465338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9e4bbde-67e5-4579-b883-bff8e4bea608/dqc_reference/reference_markers.hmm GCA_024653385.1_ASM2465338v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:00:55,907] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:00:55,909] [INFO] Found 6/6 markers.
[2023-06-30 12:00:55,982] [INFO] Query marker FASTA was written to GCA_024653385.1_ASM2465338v1_genomic.fna/markers.fasta
[2023-06-30 12:00:55,982] [INFO] Task started: Blastn
[2023-06-30 12:00:55,982] [INFO] Running command: blastn -query GCA_024653385.1_ASM2465338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e4bbde-67e5-4579-b883-bff8e4bea608/dqc_reference/reference_markers.fasta -out GCA_024653385.1_ASM2465338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:00:56,636] [INFO] Task succeeded: Blastn
[2023-06-30 12:00:56,642] [INFO] Selected 24 target genomes.
[2023-06-30 12:00:56,642] [INFO] Target genome list was writen to GCA_024653385.1_ASM2465338v1_genomic.fna/target_genomes.txt
[2023-06-30 12:00:56,647] [INFO] Task started: fastANI
[2023-06-30 12:00:56,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg41279617-2050-47ac-bf5e-8903e415997c/GCA_024653385.1_ASM2465338v1_genomic.fna.gz --refList GCA_024653385.1_ASM2465338v1_genomic.fna/target_genomes.txt --output GCA_024653385.1_ASM2465338v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:01:17,267] [INFO] Task succeeded: fastANI
[2023-06-30 12:01:17,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9e4bbde-67e5-4579-b883-bff8e4bea608/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:01:17,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9e4bbde-67e5-4579-b883-bff8e4bea608/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:01:17,294] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:01:17,295] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:01:17,295] [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
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.7937	95	1698	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.7757	133	1698	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.7507	117	1698	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.7357	134	1698	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.6524	151	1698	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	75.5765	134	1698	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.3941	80	1698	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.358	183	1698	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	75.1639	58	1698	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	74.909	69	1698	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.8197	81	1698	95	below_threshold
Actinokineospora pegani	strain=TRM 65233	GCA_009745975.1	2654637	2654637	type	True	74.7452	101	1698	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	74.7209	96	1698	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	74.7116	106	1698	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	74.702	86	1698	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	74.7005	87	1698	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	74.6424	126	1698	95	below_threshold
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	74.6381	91	1698	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:01:17,297] [INFO] DFAST Taxonomy check result was written to GCA_024653385.1_ASM2465338v1_genomic.fna/tc_result.tsv
[2023-06-30 12:01:17,298] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:01:17,298] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:01:17,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9e4bbde-67e5-4579-b883-bff8e4bea608/dqc_reference/checkm_data
[2023-06-30 12:01:17,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:01:17,366] [INFO] Task started: CheckM
[2023-06-30 12:01:17,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024653385.1_ASM2465338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024653385.1_ASM2465338v1_genomic.fna/checkm_input GCA_024653385.1_ASM2465338v1_genomic.fna/checkm_result
[2023-06-30 12:02:06,131] [INFO] Task succeeded: CheckM
[2023-06-30 12:02:06,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:02:06,159] [INFO] ===== Completeness check finished =====
[2023-06-30 12:02:06,159] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:02:06,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024653385.1_ASM2465338v1_genomic.fna/markers.fasta)
[2023-06-30 12:02:06,160] [INFO] Task started: Blastn
[2023-06-30 12:02:06,160] [INFO] Running command: blastn -query GCA_024653385.1_ASM2465338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e4bbde-67e5-4579-b883-bff8e4bea608/dqc_reference/reference_markers_gtdb.fasta -out GCA_024653385.1_ASM2465338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:02:07,151] [INFO] Task succeeded: Blastn
[2023-06-30 12:02:07,156] [INFO] Selected 24 target genomes.
[2023-06-30 12:02:07,157] [INFO] Target genome list was writen to GCA_024653385.1_ASM2465338v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:02:07,190] [INFO] Task started: fastANI
[2023-06-30 12:02:07,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg41279617-2050-47ac-bf5e-8903e415997c/GCA_024653385.1_ASM2465338v1_genomic.fna.gz --refList GCA_024653385.1_ASM2465338v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024653385.1_ASM2465338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:02:29,386] [INFO] Task succeeded: fastANI
[2023-06-30 12:02:29,414] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 12:02:29,414] [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
GCA_011367845.1	s__DSXL01 sp011367845	77.3869	410	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__DSXL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931995.1	s__JAFGDS01 sp016931995	76.6618	246	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935315.1	s__JAFGRD01 sp016935315	76.5176	277	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGRD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119795.1	s__SKOZ01 sp007119795	76.4897	131	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__SKOZ01	95.0	99.25	99.25	0.71	0.71	2	-
GCA_012744395.1	s__JAAYCB01 sp012744395	76.469	217	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAAYCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191115.1	s__JACPPG01 sp016191115	76.3392	155	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JACPPG01;g__JACPPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122045.1	s__PWXP01 sp007122045	76.325	149	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__PWXP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728855.1	s__JABWBD01 sp012728855	76.0921	233	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JABWBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016933425.1	s__UBA11386 sp016933425	76.0082	124	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__UBA11386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719125.1	s__JAAYAY01 sp012719125	75.9873	212	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAAYAY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003389325.1	s__LB-PLM-3 sp003389325	75.9267	143	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__LB-PLM-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	75.925	104	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753265.1	s__Botrimarina mediterranea	75.8436	91	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCA_015661985.1	s__SZUA-1497 sp015661985	75.8281	116	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__SZUA-1497	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515235.1	s__Anammoximicrobium sp012515235	75.7104	187	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Anammoximicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	75.6738	148	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016929515.1	s__UBA11386 sp016929515	75.6472	85	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__UBA11386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.103	63	1698	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167255.1	s__PALSA-129 sp003167255	74.8166	50	1698	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PALSA-129	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:02:29,417] [INFO] GTDB search result was written to GCA_024653385.1_ASM2465338v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:02:29,417] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:02:29,422] [INFO] DFAST_QC result json was written to GCA_024653385.1_ASM2465338v1_genomic.fna/dqc_result.json
[2023-06-30 12:02:29,422] [INFO] DFAST_QC completed!
[2023-06-30 12:02:29,422] [INFO] Total running time: 0h1m52s