[2024-01-24 11:59:22,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgcee84e76-9e40-4adb-8ad8-ecf054535285/dqc_reference
[2024-01-24 11:59:25,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,643] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b3ea365-2f27-45f2-9f64-4349f00953bc/GCF_003862495.1_ASM386249v1_genomic.fna.gz | prodigal -d GCF_003862495.1_ASM386249v1_genomic.fna/cds.fna -a GCF_003862495.1_ASM386249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:46,174] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:46,174] [INFO] Task started: HMMsearch
[2024-01-24 11:59:46,174] [INFO] Running command: hmmsearch --tblout GCF_003862495.1_ASM386249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcee84e76-9e40-4adb-8ad8-ecf054535285/dqc_reference/reference_markers.hmm GCF_003862495.1_ASM386249v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:46,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:46,416] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8b3ea365-2f27-45f2-9f64-4349f00953bc/GCF_003862495.1_ASM386249v1_genomic.fna.gz]
[2024-01-24 11:59:46,449] [INFO] Query marker FASTA was written to GCF_003862495.1_ASM386249v1_genomic.fna/markers.fasta
[2024-01-24 11:59:46,450] [INFO] Task started: Blastn
[2024-01-24 11:59:46,450] [INFO] Running command: blastn -query GCF_003862495.1_ASM386249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcee84e76-9e40-4adb-8ad8-ecf054535285/dqc_reference/reference_markers.fasta -out GCF_003862495.1_ASM386249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:46,943] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:46,947] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:46,948] [INFO] Target genome list was writen to GCF_003862495.1_ASM386249v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:46,954] [INFO] Task started: fastANI
[2024-01-24 11:59:46,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b3ea365-2f27-45f2-9f64-4349f00953bc/GCF_003862495.1_ASM386249v1_genomic.fna.gz --refList GCF_003862495.1_ASM386249v1_genomic.fna/target_genomes.txt --output GCF_003862495.1_ASM386249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:54,456] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:54,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcee84e76-9e40-4adb-8ad8-ecf054535285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:54,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcee84e76-9e40-4adb-8ad8-ecf054535285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:54,472] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:54,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:54,473] [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
Halocatena pleomorpha	strain=SPP-AMP-1	GCA_003862495.1	1785090	1785090	type	True	100.0	1183	1186	95	conclusive
Halorussus ruber	strain=YC25	GCA_004765785.1	1126238	1126238	type	True	76.4997	94	1186	95	below_threshold
Halorussus pelagicus	strain=RC-68	GCA_004087835.1	2505977	2505977	type	True	76.3755	73	1186	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	76.2833	122	1186	95	below_threshold
Halococcus qingdaonensis	strain=CGMCC 1.4243	GCA_024508235.1	224402	224402	type	True	76.2606	110	1186	95	below_threshold
Halococcus salsus	strain=ZJ1	GCA_009900715.1	2162894	2162894	type	True	76.2371	101	1186	95	below_threshold
Halococcoides cellulosivorans	strain=HArcel1	GCA_003058365.1	1679096	1679096	type	True	76.2155	63	1186	95	below_threshold
Halorussus litoreus	strain=HD8-51	GCA_003382685.1	1710536	1710536	type	True	76.175	105	1186	95	below_threshold
Halorubrum halodurans	strain=Cb34	GCA_002252985.1	1383851	1383851	type	True	76.1335	83	1186	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	75.9761	92	1186	95	below_threshold
Halalkalirubrum salinum	strain=N1521	GCA_005543295.1	2563889	2563889	type	True	75.8559	67	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:54,474] [INFO] DFAST Taxonomy check result was written to GCF_003862495.1_ASM386249v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:54,474] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:54,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:54,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcee84e76-9e40-4adb-8ad8-ecf054535285/dqc_reference/checkm_data
[2024-01-24 11:59:54,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:54,511] [INFO] Task started: CheckM
[2024-01-24 11:59:54,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003862495.1_ASM386249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003862495.1_ASM386249v1_genomic.fna/checkm_input GCF_003862495.1_ASM386249v1_genomic.fna/checkm_result
[2024-01-24 12:00:52,598] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:52,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:52,620] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:52,621] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:52,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003862495.1_ASM386249v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:52,622] [INFO] Task started: Blastn
[2024-01-24 12:00:52,622] [INFO] Running command: blastn -query GCF_003862495.1_ASM386249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcee84e76-9e40-4adb-8ad8-ecf054535285/dqc_reference/reference_markers_gtdb.fasta -out GCF_003862495.1_ASM386249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:53,029] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:53,033] [INFO] Selected 13 target genomes.
[2024-01-24 12:00:53,033] [INFO] Target genome list was writen to GCF_003862495.1_ASM386249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:53,046] [INFO] Task started: fastANI
[2024-01-24 12:00:53,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b3ea365-2f27-45f2-9f64-4349f00953bc/GCF_003862495.1_ASM386249v1_genomic.fna.gz --refList GCF_003862495.1_ASM386249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003862495.1_ASM386249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:00,218] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:00,234] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:00,234] [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_003862495.1	s__Halomarina oriensis_A	100.0	1183	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004765785.1	s__Halorussus ruber	76.4777	95	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000496215.1	s__Halonotius sp000496215	76.4117	65	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	96.16	96.16	0.87	0.87	2	-
GCF_004087835.1	s__Halorussus sp004087835	76.3794	74	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023185.1	s__CBA1134 sp003023185	76.2457	74	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003058365.1	s__HARCEL1 sp003058365	76.2155	63	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__HARCEL1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382685.1	s__Halorussus litoreus	76.175	105	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005239435.1	s__Halorussus sp005239435	76.1582	99	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252985.1	s__Halorubrum halodurans	76.1335	83	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	75.9761	92	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005543295.1	s__Halalkalirubrum salinum	75.8559	67	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halalkalirubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:00,236] [INFO] GTDB search result was written to GCF_003862495.1_ASM386249v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:00,236] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:00,243] [INFO] DFAST_QC result json was written to GCF_003862495.1_ASM386249v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:00,243] [INFO] DFAST_QC completed!
[2024-01-24 12:01:00,243] [INFO] Total running time: 0h1m37s