[2024-01-24 13:40:31,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:31,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:31,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg0440fde1-30b3-4bfc-84d9-7cd090a0e38a/dqc_reference
[2024-01-24 13:40:33,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:33,097] [INFO] Task started: Prodigal
[2024-01-24 13:40:33,097] [INFO] Running command: gunzip -c /var/lib/cwl/stgfea44dcd-4051-4a19-bc64-c1eb0344e241/GCF_004681185.1_ASM468118v1_genomic.fna.gz | prodigal -d GCF_004681185.1_ASM468118v1_genomic.fna/cds.fna -a GCF_004681185.1_ASM468118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:59,381] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:59,381] [INFO] Task started: HMMsearch
[2024-01-24 13:40:59,382] [INFO] Running command: hmmsearch --tblout GCF_004681185.1_ASM468118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0440fde1-30b3-4bfc-84d9-7cd090a0e38a/dqc_reference/reference_markers.hmm GCF_004681185.1_ASM468118v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:59,733] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:59,734] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfea44dcd-4051-4a19-bc64-c1eb0344e241/GCF_004681185.1_ASM468118v1_genomic.fna.gz]
[2024-01-24 13:40:59,777] [INFO] Query marker FASTA was written to GCF_004681185.1_ASM468118v1_genomic.fna/markers.fasta
[2024-01-24 13:40:59,777] [INFO] Task started: Blastn
[2024-01-24 13:40:59,777] [INFO] Running command: blastn -query GCF_004681185.1_ASM468118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0440fde1-30b3-4bfc-84d9-7cd090a0e38a/dqc_reference/reference_markers.fasta -out GCF_004681185.1_ASM468118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:00,342] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:00,347] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:00,347] [INFO] Target genome list was writen to GCF_004681185.1_ASM468118v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:00,351] [INFO] Task started: fastANI
[2024-01-24 13:41:00,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgfea44dcd-4051-4a19-bc64-c1eb0344e241/GCF_004681185.1_ASM468118v1_genomic.fna.gz --refList GCF_004681185.1_ASM468118v1_genomic.fna/target_genomes.txt --output GCF_004681185.1_ASM468118v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:09,477] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:09,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0440fde1-30b3-4bfc-84d9-7cd090a0e38a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:09,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0440fde1-30b3-4bfc-84d9-7cd090a0e38a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:09,487] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:09,487] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:09,487] [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 amylolytica	strain=LR21	GCA_004681185.1	2562280	2562280	type	True	100.0	1662	1663	95	conclusive
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	89.6602	1104	1663	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	89.4781	1210	1663	95	below_threshold
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	83.2211	880	1663	95	below_threshold
Halomicroarcula pellucida	strain=JCM 17820	GCA_014647235.1	1427151	1427151	type	True	83.0535	863	1663	95	below_threshold
Halomicroarcula pellucida	strain=CECT 7537	GCA_019599515.1	1427151	1427151	type	True	82.9943	870	1663	95	below_threshold
Haloarcula salaria	strain=JCM 15759	GCA_014647095.1	575195	575195	type	True	80.0579	568	1663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:09,489] [INFO] DFAST Taxonomy check result was written to GCF_004681185.1_ASM468118v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:09,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:09,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:09,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0440fde1-30b3-4bfc-84d9-7cd090a0e38a/dqc_reference/checkm_data
[2024-01-24 13:41:09,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:09,562] [INFO] Task started: CheckM
[2024-01-24 13:41:09,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004681185.1_ASM468118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004681185.1_ASM468118v1_genomic.fna/checkm_input GCF_004681185.1_ASM468118v1_genomic.fna/checkm_result
[2024-01-24 13:42:19,510] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:19,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:19,536] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:19,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:19,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004681185.1_ASM468118v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:19,538] [INFO] Task started: Blastn
[2024-01-24 13:42:19,538] [INFO] Running command: blastn -query GCF_004681185.1_ASM468118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0440fde1-30b3-4bfc-84d9-7cd090a0e38a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004681185.1_ASM468118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:20,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:20,037] [INFO] Selected 8 target genomes.
[2024-01-24 13:42:20,037] [INFO] Target genome list was writen to GCF_004681185.1_ASM468118v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:20,060] [INFO] Task started: fastANI
[2024-01-24 13:42:20,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgfea44dcd-4051-4a19-bc64-c1eb0344e241/GCF_004681185.1_ASM468118v1_genomic.fna.gz --refList GCF_004681185.1_ASM468118v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004681185.1_ASM468118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:28,024] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:28,032] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:28,032] [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_004681185.1	s__Halomicroarcula amylolytica	100.0	1662	1663	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010119205.1	s__Halomicroarcula limicola	89.6488	1104	1663	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014647235.1	s__Halomicroarcula pellucida	83.0273	867	1663	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	96.63	96.63	0.87	0.87	2	-
GCF_010119195.1	s__Haloarcula salina	81.5035	707	1663	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005406125.1	s__Haloarcula sp005406125	81.0598	661	1663	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	80.3531	638	1663	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.3005	N/A	N/A	N/A	N/A	1	-
GCF_002844335.1	s__Haloarcula taiwanensis	80.2153	605	1663	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.00	98.44	0.94	0.92	4	-
GCA_000336895.1	s__Haloarcula argentinensis	79.8657	588	1663	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	99.05	99.05	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:28,034] [INFO] GTDB search result was written to GCF_004681185.1_ASM468118v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:28,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:28,037] [INFO] DFAST_QC result json was written to GCF_004681185.1_ASM468118v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:28,037] [INFO] DFAST_QC completed!
[2024-01-24 13:42:28,038] [INFO] Total running time: 0h1m56s