[2024-01-24 12:37:25,004] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:25,008] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:25,008] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe6d9587-afbe-4f0e-93b6-042089c5679e/dqc_reference
[2024-01-24 12:37:26,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,281] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,281] [INFO] Running command: gunzip -c /var/lib/cwl/stga0a7b6e3-f622-4484-8f34-f0f020e7ec3a/GCF_019061225.1_ASM1906122v1_genomic.fna.gz | prodigal -d GCF_019061225.1_ASM1906122v1_genomic.fna/cds.fna -a GCF_019061225.1_ASM1906122v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:44,094] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:44,095] [INFO] Task started: HMMsearch
[2024-01-24 12:37:44,095] [INFO] Running command: hmmsearch --tblout GCF_019061225.1_ASM1906122v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe6d9587-afbe-4f0e-93b6-042089c5679e/dqc_reference/reference_markers.hmm GCF_019061225.1_ASM1906122v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:44,331] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:44,332] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga0a7b6e3-f622-4484-8f34-f0f020e7ec3a/GCF_019061225.1_ASM1906122v1_genomic.fna.gz]
[2024-01-24 12:37:44,368] [INFO] Query marker FASTA was written to GCF_019061225.1_ASM1906122v1_genomic.fna/markers.fasta
[2024-01-24 12:37:44,369] [INFO] Task started: Blastn
[2024-01-24 12:37:44,369] [INFO] Running command: blastn -query GCF_019061225.1_ASM1906122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe6d9587-afbe-4f0e-93b6-042089c5679e/dqc_reference/reference_markers.fasta -out GCF_019061225.1_ASM1906122v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:44,899] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:44,903] [INFO] Selected 10 target genomes.
[2024-01-24 12:37:44,903] [INFO] Target genome list was writen to GCF_019061225.1_ASM1906122v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:44,910] [INFO] Task started: fastANI
[2024-01-24 12:37:44,910] [INFO] Running command: fastANI --query /var/lib/cwl/stga0a7b6e3-f622-4484-8f34-f0f020e7ec3a/GCF_019061225.1_ASM1906122v1_genomic.fna.gz --refList GCF_019061225.1_ASM1906122v1_genomic.fna/target_genomes.txt --output GCF_019061225.1_ASM1906122v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:54,613] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:54,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe6d9587-afbe-4f0e-93b6-042089c5679e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:54,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe6d9587-afbe-4f0e-93b6-042089c5679e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:54,631] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:54,631] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:54,632] [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
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	100.0	1259	1259	95	conclusive
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	99.994	1250	1259	95	conclusive
Haloarcula amylolytica	strain=JCM 13557	GCA_000336615.1	396317	396317	type	True	84.1099	838	1259	95	below_threshold
Haloarcula mannanilytica	strain=MD130-1	GCA_005406125.1	2509225	2509225	type	True	84.1093	873	1259	95	below_threshold
Haloarcula rubripromontorii	strain=SL3	GCA_001280425.1	1705562	1705562	type	True	83.8853	818	1259	95	below_threshold
Haloarcula hispanica	strain=CGMCC 1.2049	GCA_000223905.1	51589	51589	type	True	83.8477	833	1259	95	below_threshold
Haloarcula salaria	strain=JCM 15759	GCA_014647095.1	575195	575195	type	True	83.3182	767	1259	95	below_threshold
Haloarcula sebkhae	strain=JCM 19018	GCA_014647415.1	932660	932660	type	True	83.2617	792	1259	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	82.5555	755	1259	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	82.4631	745	1259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:54,635] [INFO] DFAST Taxonomy check result was written to GCF_019061225.1_ASM1906122v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:54,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:54,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:54,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe6d9587-afbe-4f0e-93b6-042089c5679e/dqc_reference/checkm_data
[2024-01-24 12:37:54,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:54,679] [INFO] Task started: CheckM
[2024-01-24 12:37:54,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019061225.1_ASM1906122v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019061225.1_ASM1906122v1_genomic.fna/checkm_input GCF_019061225.1_ASM1906122v1_genomic.fna/checkm_result
[2024-01-24 12:38:43,722] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:43,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:43,743] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:43,743] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:43,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019061225.1_ASM1906122v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:43,744] [INFO] Task started: Blastn
[2024-01-24 12:38:43,744] [INFO] Running command: blastn -query GCF_019061225.1_ASM1906122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe6d9587-afbe-4f0e-93b6-042089c5679e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019061225.1_ASM1906122v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:44,289] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:44,293] [INFO] Selected 11 target genomes.
[2024-01-24 12:38:44,294] [INFO] Target genome list was writen to GCF_019061225.1_ASM1906122v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:44,303] [INFO] Task started: fastANI
[2024-01-24 12:38:44,303] [INFO] Running command: fastANI --query /var/lib/cwl/stga0a7b6e3-f622-4484-8f34-f0f020e7ec3a/GCF_019061225.1_ASM1906122v1_genomic.fna.gz --refList GCF_019061225.1_ASM1906122v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019061225.1_ASM1906122v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:53,823] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:53,835] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:53,835] [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_010119195.1	s__Haloarcula salina	99.994	1250	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_005406125.1	s__Haloarcula sp005406125	84.1093	873	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336615.1	s__Haloarcula amylolytica	84.0625	843	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.3005	N/A	N/A	N/A	N/A	1	-
GCF_001280425.1	s__Haloarcula rubripromontorii	83.8968	817	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.01	99.01	0.90	0.90	2	-
GCF_000223905.1	s__Haloarcula hispanica	83.8448	833	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.3005	98.55	97.98	0.94	0.91	11	-
GCF_002844335.1	s__Haloarcula taiwanensis	83.8197	799	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.00	98.44	0.94	0.92	4	-
GCF_008729015.1	s__Haloarcula sp008729015	83.404	804	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014647415.1	s__Haloarcula sebkhae	83.2807	790	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	95.97	95.97	0.88	0.88	2	-
GCA_000336895.1	s__Haloarcula argentinensis	83.1086	791	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	99.05	99.05	0.91	0.91	2	-
GCF_010119205.1	s__Halomicroarcula limicola	82.5958	751	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003021755.1	s__Halomicroarcula sp003021755	81.1952	401	1259	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:53,837] [INFO] GTDB search result was written to GCF_019061225.1_ASM1906122v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:53,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:53,841] [INFO] DFAST_QC result json was written to GCF_019061225.1_ASM1906122v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:53,841] [INFO] DFAST_QC completed!
[2024-01-24 12:38:53,841] [INFO] Total running time: 0h1m29s