[2024-01-25 19:58:05,422] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:05,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:05,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a16cd2f-65e5-483a-937d-426300604938/dqc_reference
[2024-01-25 19:58:06,543] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:06,544] [INFO] Task started: Prodigal
[2024-01-25 19:58:06,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg999ec6e0-acf1-47f8-985b-46ebce0e8c96/GCF_002554705.1_ASM255470v1_genomic.fna.gz | prodigal -d GCF_002554705.1_ASM255470v1_genomic.fna/cds.fna -a GCF_002554705.1_ASM255470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:27,312] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:27,312] [INFO] Task started: HMMsearch
[2024-01-25 19:58:27,312] [INFO] Running command: hmmsearch --tblout GCF_002554705.1_ASM255470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a16cd2f-65e5-483a-937d-426300604938/dqc_reference/reference_markers.hmm GCF_002554705.1_ASM255470v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:27,511] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:27,512] [INFO] Found 6/6 markers.
[2024-01-25 19:58:27,539] [INFO] Query marker FASTA was written to GCF_002554705.1_ASM255470v1_genomic.fna/markers.fasta
[2024-01-25 19:58:27,539] [INFO] Task started: Blastn
[2024-01-25 19:58:27,539] [INFO] Running command: blastn -query GCF_002554705.1_ASM255470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a16cd2f-65e5-483a-937d-426300604938/dqc_reference/reference_markers.fasta -out GCF_002554705.1_ASM255470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:28,172] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:28,175] [INFO] Selected 21 target genomes.
[2024-01-25 19:58:28,175] [INFO] Target genome list was writen to GCF_002554705.1_ASM255470v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:28,215] [INFO] Task started: fastANI
[2024-01-25 19:58:28,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg999ec6e0-acf1-47f8-985b-46ebce0e8c96/GCF_002554705.1_ASM255470v1_genomic.fna.gz --refList GCF_002554705.1_ASM255470v1_genomic.fna/target_genomes.txt --output GCF_002554705.1_ASM255470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:42,706] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:42,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a16cd2f-65e5-483a-937d-426300604938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:42,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a16cd2f-65e5-483a-937d-426300604938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:42,714] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:42,714] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:42,714] [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
Longimonas halophila	strain=KCTC 42399	GCA_002554705.1	1469170	1469170	type	True	100.0	1225	1226	95	conclusive
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	76.744	178	1226	95	below_threshold
Longibacter salinarum	strain=KCTC 52045	GCA_002554795.1	1850348	1850348	type	True	76.5796	93	1226	95	below_threshold
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	76.4817	128	1226	95	below_threshold
Salinibacter altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	76.3791	115	1226	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	75.9491	78	1226	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	75.7753	51	1226	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	75.7021	54	1226	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:42,716] [INFO] DFAST Taxonomy check result was written to GCF_002554705.1_ASM255470v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:42,718] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:42,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:42,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a16cd2f-65e5-483a-937d-426300604938/dqc_reference/checkm_data
[2024-01-25 19:58:42,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:42,757] [INFO] Task started: CheckM
[2024-01-25 19:58:42,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002554705.1_ASM255470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002554705.1_ASM255470v1_genomic.fna/checkm_input GCF_002554705.1_ASM255470v1_genomic.fna/checkm_result
[2024-01-25 19:59:38,876] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:38,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:38,906] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:38,906] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:38,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002554705.1_ASM255470v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:38,907] [INFO] Task started: Blastn
[2024-01-25 19:59:38,907] [INFO] Running command: blastn -query GCF_002554705.1_ASM255470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a16cd2f-65e5-483a-937d-426300604938/dqc_reference/reference_markers_gtdb.fasta -out GCF_002554705.1_ASM255470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:39,935] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:39,940] [INFO] Selected 20 target genomes.
[2024-01-25 19:59:39,940] [INFO] Target genome list was writen to GCF_002554705.1_ASM255470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:39,959] [INFO] Task started: fastANI
[2024-01-25 19:59:39,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg999ec6e0-acf1-47f8-985b-46ebce0e8c96/GCF_002554705.1_ASM255470v1_genomic.fna.gz --refList GCF_002554705.1_ASM255470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002554705.1_ASM255470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:51,342] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:51,353] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:51,353] [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_002554705.1	s__Longimonas halophila	100.0	1225	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Longimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003022565.1	s__Salinibacter sp003022565	76.7924	88	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419585.1	s__Salisaeta longa	76.743	178	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salisaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002894685.1	s__Salinibacter luteus	76.5898	139	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	96.2585	N/A	N/A	N/A	N/A	1	-
GCA_009908415.1	s__JAAAPH01 sp009908415	76.581	144	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002554795.1	s__Longibacter salinarum	76.5796	93	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Longibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954405.1	s__Salinibacter sp002954405	76.5608	104	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002894665.1	s__Salinibacter iranicus	76.4206	135	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	96.2585	N/A	N/A	N/A	N/A	1	-
GCF_002894645.1	s__Salinibacter altiplanensis	76.3791	115	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	98.33	98.12	0.91	0.90	3	-
GCA_003023275.1	s__QS-8-64-10 sp003023275	76.2128	72	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__QS-8-64-10	95.0	97.61	97.46	0.68	0.68	3	-
GCA_009908725.1	s__Longibacter sp009908725	76.2045	86	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Longibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018609755.1	s__Salinibacter sp018609755	76.1464	108	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022435.1	s__Salinibacter sp003022435	76.0968	97	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	75.7753	51	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022655.1	s__Salinibacter sp003022655	75.7484	69	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022535.1	s__QS-8-64-10 sp003022535	75.7258	52	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__QS-8-64-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022485.1	s__QS-8-64-10 sp003022485	75.5578	73	1226	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__QS-8-64-10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:51,354] [INFO] GTDB search result was written to GCF_002554705.1_ASM255470v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:51,355] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:51,357] [INFO] DFAST_QC result json was written to GCF_002554705.1_ASM255470v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:51,358] [INFO] DFAST_QC completed!
[2024-01-25 19:59:51,358] [INFO] Total running time: 0h1m46s