[2024-01-25 19:57:20,783] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:20,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:20,785] [INFO] DQC Reference Directory: /var/lib/cwl/stgecfbefba-3711-42cd-b2ef-6218cb7d8b9e/dqc_reference
[2024-01-25 19:57:21,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:21,911] [INFO] Task started: Prodigal
[2024-01-25 19:57:21,912] [INFO] Running command: gunzip -c /var/lib/cwl/stgacbcbd1a-572b-42dc-9027-ced690bd8893/GCF_000337815.1_ASM33781v1_genomic.fna.gz | prodigal -d GCF_000337815.1_ASM33781v1_genomic.fna/cds.fna -a GCF_000337815.1_ASM33781v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:36,645] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:36,645] [INFO] Task started: HMMsearch
[2024-01-25 19:57:36,645] [INFO] Running command: hmmsearch --tblout GCF_000337815.1_ASM33781v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecfbefba-3711-42cd-b2ef-6218cb7d8b9e/dqc_reference/reference_markers.hmm GCF_000337815.1_ASM33781v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:36,860] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:36,861] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgacbcbd1a-572b-42dc-9027-ced690bd8893/GCF_000337815.1_ASM33781v1_genomic.fna.gz]
[2024-01-25 19:57:36,891] [INFO] Query marker FASTA was written to GCF_000337815.1_ASM33781v1_genomic.fna/markers.fasta
[2024-01-25 19:57:36,891] [INFO] Task started: Blastn
[2024-01-25 19:57:36,892] [INFO] Running command: blastn -query GCF_000337815.1_ASM33781v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecfbefba-3711-42cd-b2ef-6218cb7d8b9e/dqc_reference/reference_markers.fasta -out GCF_000337815.1_ASM33781v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:37,384] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:37,386] [INFO] Selected 6 target genomes.
[2024-01-25 19:57:37,387] [INFO] Target genome list was writen to GCF_000337815.1_ASM33781v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:37,390] [INFO] Task started: fastANI
[2024-01-25 19:57:37,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgacbcbd1a-572b-42dc-9027-ced690bd8893/GCF_000337815.1_ASM33781v1_genomic.fna.gz --refList GCF_000337815.1_ASM33781v1_genomic.fna/target_genomes.txt --output GCF_000337815.1_ASM33781v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:42,615] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:42,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecfbefba-3711-42cd-b2ef-6218cb7d8b9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:42,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecfbefba-3711-42cd-b2ef-6218cb7d8b9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:42,621] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:42,621] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:42,621] [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
Haloferax mucosum	strain=ATCC BAA-1512	GCA_000337815.1	403181	403181	type	True	100.0	1113	1114	95	conclusive
Haloferax mediterranei	strain=CGMCC 1.2087	GCA_000306765.2	2252	2252	type	True	86.1686	899	1114	95	below_threshold
Haloferax mediterranei	strain=ATCC 33500	GCA_000337295.1	2252	2252	type	True	86.1588	898	1114	95	below_threshold
Haloferax mediterranei	strain=ATCC 33500	GCA_005406325.1	2252	2252	type	True	86.1276	907	1114	95	below_threshold
Haloferax mediterranei	strain=ATCC 33500	GCA_000685635.1	2252	2252	type	True	86.1109	911	1114	95	below_threshold
Haloferax marisrubri	strain=SB3	GCA_001469875.2	1544719	1544719	type	True	84.4266	802	1114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:42,622] [INFO] DFAST Taxonomy check result was written to GCF_000337815.1_ASM33781v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:42,623] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:42,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:42,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecfbefba-3711-42cd-b2ef-6218cb7d8b9e/dqc_reference/checkm_data
[2024-01-25 19:57:42,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:42,661] [INFO] Task started: CheckM
[2024-01-25 19:57:42,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337815.1_ASM33781v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337815.1_ASM33781v1_genomic.fna/checkm_input GCF_000337815.1_ASM33781v1_genomic.fna/checkm_result
[2024-01-25 19:58:23,817] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:23,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:23,839] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:23,839] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:23,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337815.1_ASM33781v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:23,840] [INFO] Task started: Blastn
[2024-01-25 19:58:23,840] [INFO] Running command: blastn -query GCF_000337815.1_ASM33781v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecfbefba-3711-42cd-b2ef-6218cb7d8b9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337815.1_ASM33781v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:24,359] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:24,362] [INFO] Selected 10 target genomes.
[2024-01-25 19:58:24,362] [INFO] Target genome list was writen to GCF_000337815.1_ASM33781v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:24,368] [INFO] Task started: fastANI
[2024-01-25 19:58:24,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgacbcbd1a-572b-42dc-9027-ced690bd8893/GCF_000337815.1_ASM33781v1_genomic.fna.gz --refList GCF_000337815.1_ASM33781v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337815.1_ASM33781v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:33,217] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:33,224] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:33,224] [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_000337815.1	s__Haloferax mucosum	100.0	1113	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000306765.2	s__Haloferax mediterranei	86.1783	898	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	99.99	99.97	1.00	0.99	4	-
GCF_000337835.1	s__Haloferax sulfurifontis	84.5806	752	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.9285	99.04	99.04	0.92	0.92	2	-
GCF_001469875.2	s__Haloferax marisrubri	84.4234	802	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	95.85	95.85	0.83	0.83	2	-
GCF_001368915.1	s__Haloferax massiliensis	84.4215	767	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.2845	98.47	96.94	0.94	0.88	3	-
GCF_000336815.1	s__Haloferax prahovense	84.3679	791	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	99.29	99.22	0.91	0.91	5	-
GCF_001482285.1	s__Haloferax sp001482285	84.183	793	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336955.1	s__Haloferax larsenii	83.2784	764	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	96.49	96.49	0.91	0.91	2	-
GCF_000336755.1	s__Haloferax elongans	83.0622	767	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674585.1	s__Haloferax sp009674585	82.8077	699	1114	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:33,225] [INFO] GTDB search result was written to GCF_000337815.1_ASM33781v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:33,226] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:33,228] [INFO] DFAST_QC result json was written to GCF_000337815.1_ASM33781v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:33,228] [INFO] DFAST_QC completed!
[2024-01-25 19:58:33,228] [INFO] Total running time: 0h1m12s