[2024-01-24 11:26:28,082] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,083] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b81aee3-58e7-4a6c-80c3-781096ecc8b4/dqc_reference
[2024-01-24 11:26:29,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,540] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg91764b67-e661-46e5-96a9-6e42fc39349c/GCF_026965555.1_ASM2696555v1_genomic.fna.gz | prodigal -d GCF_026965555.1_ASM2696555v1_genomic.fna/cds.fna -a GCF_026965555.1_ASM2696555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:07,916] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:07,916] [INFO] Task started: HMMsearch
[2024-01-24 11:27:07,917] [INFO] Running command: hmmsearch --tblout GCF_026965555.1_ASM2696555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b81aee3-58e7-4a6c-80c3-781096ecc8b4/dqc_reference/reference_markers.hmm GCF_026965555.1_ASM2696555v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:08,407] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:08,408] [INFO] Found 6/6 markers.
[2024-01-24 11:27:08,499] [INFO] Query marker FASTA was written to GCF_026965555.1_ASM2696555v1_genomic.fna/markers.fasta
[2024-01-24 11:27:08,499] [INFO] Task started: Blastn
[2024-01-24 11:27:08,499] [INFO] Running command: blastn -query GCF_026965555.1_ASM2696555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b81aee3-58e7-4a6c-80c3-781096ecc8b4/dqc_reference/reference_markers.fasta -out GCF_026965555.1_ASM2696555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:09,344] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:09,348] [INFO] Selected 31 target genomes.
[2024-01-24 11:27:09,348] [INFO] Target genome list was writen to GCF_026965555.1_ASM2696555v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:09,358] [INFO] Task started: fastANI
[2024-01-24 11:27:09,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg91764b67-e661-46e5-96a9-6e42fc39349c/GCF_026965555.1_ASM2696555v1_genomic.fna.gz --refList GCF_026965555.1_ASM2696555v1_genomic.fna/target_genomes.txt --output GCF_026965555.1_ASM2696555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:51,475] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:51,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b81aee3-58e7-4a6c-80c3-781096ecc8b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:51,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b81aee3-58e7-4a6c-80c3-781096ecc8b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:51,503] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:51,503] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:51,504] [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
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	91.0336	3266	4409	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	91.015	3352	4409	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	76.1778	1230	4409	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.428	364	4409	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	75.159	103	4409	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1129	795	4409	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	75.1057	196	4409	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	75.1033	105	4409	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	75.0989	525	4409	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	75.0744	569	4409	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.0743	637	4409	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.0461	437	4409	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	75.0111	241	4409	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	75.0041	572	4409	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	74.9814	430	4409	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	74.9675	104	4409	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	74.9445	284	4409	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	74.9439	221	4409	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	74.937	432	4409	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	74.9296	202	4409	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	74.9239	484	4409	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	74.9145	205	4409	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	74.9142	381	4409	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	74.8835	872	4409	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	74.8559	878	4409	95	below_threshold
Streptomyces bambusae	strain=T110	GCA_020532645.1	1550616	1550616	type	True	74.8535	719	4409	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	74.8366	670	4409	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	74.8159	180	4409	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	74.8122	223	4409	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	74.8071	198	4409	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	74.7988	836	4409	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:51,506] [INFO] DFAST Taxonomy check result was written to GCF_026965555.1_ASM2696555v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:51,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:51,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:51,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b81aee3-58e7-4a6c-80c3-781096ecc8b4/dqc_reference/checkm_data
[2024-01-24 11:27:51,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:51,636] [INFO] Task started: CheckM
[2024-01-24 11:27:51,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026965555.1_ASM2696555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026965555.1_ASM2696555v1_genomic.fna/checkm_input GCF_026965555.1_ASM2696555v1_genomic.fna/checkm_result
[2024-01-24 11:30:32,523] [INFO] Task succeeded: CheckM
[2024-01-24 11:30:32,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:30:32,553] [INFO] ===== Completeness check finished =====
[2024-01-24 11:30:32,554] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:30:32,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026965555.1_ASM2696555v1_genomic.fna/markers.fasta)
[2024-01-24 11:30:32,555] [INFO] Task started: Blastn
[2024-01-24 11:30:32,555] [INFO] Running command: blastn -query GCF_026965555.1_ASM2696555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b81aee3-58e7-4a6c-80c3-781096ecc8b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_026965555.1_ASM2696555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:30:33,925] [INFO] Task succeeded: Blastn
[2024-01-24 11:30:33,929] [INFO] Selected 7 target genomes.
[2024-01-24 11:30:33,930] [INFO] Target genome list was writen to GCF_026965555.1_ASM2696555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:30:33,937] [INFO] Task started: fastANI
[2024-01-24 11:30:33,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg91764b67-e661-46e5-96a9-6e42fc39349c/GCF_026965555.1_ASM2696555v1_genomic.fna.gz --refList GCF_026965555.1_ASM2696555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026965555.1_ASM2696555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:30:58,347] [INFO] Task succeeded: fastANI
[2024-01-24 11:30:58,355] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:30:58,355] [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_002343915.1	s__Nannocystis exedens	91.0311	3350	4409	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013812955.1	s__Nannocystis sp013812955	79.7998	1206	4409	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793465.1	s__Nannocystis sp016793465	79.4166	2038	4409	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714285.1	s__Nannocystis sp016714285	79.2919	1766	4409	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCA_016712315.1	s__JADJRG01 sp016712315	76.7255	1220	4409	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464385.1	s__Ga0077550 sp001464385	76.1496	1366	4409	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	75.3444	1371	4409	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:30:58,357] [INFO] GTDB search result was written to GCF_026965555.1_ASM2696555v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:30:58,358] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:30:58,362] [INFO] DFAST_QC result json was written to GCF_026965555.1_ASM2696555v1_genomic.fna/dqc_result.json
[2024-01-24 11:30:58,362] [INFO] DFAST_QC completed!
[2024-01-24 11:30:58,362] [INFO] Total running time: 0h4m30s