[2024-01-25 19:44:05,617] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:05,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:05,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg35f09e0b-9ee2-4609-8fc9-a2bdedf2cf0b/dqc_reference
[2024-01-25 19:44:06,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:06,781] [INFO] Task started: Prodigal
[2024-01-25 19:44:06,781] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d555171-60c1-4396-9bc5-ff566b1522f5/GCF_023077655.1_ASM2307765v1_genomic.fna.gz | prodigal -d GCF_023077655.1_ASM2307765v1_genomic.fna/cds.fna -a GCF_023077655.1_ASM2307765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:26,604] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:26,605] [INFO] Task started: HMMsearch
[2024-01-25 19:44:26,605] [INFO] Running command: hmmsearch --tblout GCF_023077655.1_ASM2307765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35f09e0b-9ee2-4609-8fc9-a2bdedf2cf0b/dqc_reference/reference_markers.hmm GCF_023077655.1_ASM2307765v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:26,836] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:26,837] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1d555171-60c1-4396-9bc5-ff566b1522f5/GCF_023077655.1_ASM2307765v1_genomic.fna.gz]
[2024-01-25 19:44:26,881] [INFO] Query marker FASTA was written to GCF_023077655.1_ASM2307765v1_genomic.fna/markers.fasta
[2024-01-25 19:44:26,881] [INFO] Task started: Blastn
[2024-01-25 19:44:26,881] [INFO] Running command: blastn -query GCF_023077655.1_ASM2307765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35f09e0b-9ee2-4609-8fc9-a2bdedf2cf0b/dqc_reference/reference_markers.fasta -out GCF_023077655.1_ASM2307765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:27,374] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:27,377] [INFO] Selected 8 target genomes.
[2024-01-25 19:44:27,377] [INFO] Target genome list was writen to GCF_023077655.1_ASM2307765v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:27,389] [INFO] Task started: fastANI
[2024-01-25 19:44:27,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d555171-60c1-4396-9bc5-ff566b1522f5/GCF_023077655.1_ASM2307765v1_genomic.fna.gz --refList GCF_023077655.1_ASM2307765v1_genomic.fna/target_genomes.txt --output GCF_023077655.1_ASM2307765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:35,481] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:35,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35f09e0b-9ee2-4609-8fc9-a2bdedf2cf0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:35,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35f09e0b-9ee2-4609-8fc9-a2bdedf2cf0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:35,489] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:35,489] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:35,489] [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
Halorientalis brevis	strain=YC89	GCA_023077655.1	1126241	1126241	type	True	100.0	1448	1526	95	conclusive
Halorientalis salina	strain=NEN8	GCA_023566035.1	2932266	2932266	type	True	83.7848	854	1526	95	below_threshold
Halorientalis salina	strain=NEN8	GCA_005049285.1	2932266	2932266	type	True	83.7841	854	1526	95	below_threshold
Halorientalis persicus	strain=IBRC-M 10043	GCA_900110215.1	1367881	1367881	type	True	80.423	695	1526	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	80.3439	690	1526	95	below_threshold
Halorientalis marina	strain=GDY88	GCA_023028345.1	2931976	2931976	type	True	80.1498	677	1526	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	78.4097	535	1526	95	below_threshold
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	78.0679	435	1526	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:35,490] [INFO] DFAST Taxonomy check result was written to GCF_023077655.1_ASM2307765v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:35,491] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:35,491] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:35,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35f09e0b-9ee2-4609-8fc9-a2bdedf2cf0b/dqc_reference/checkm_data
[2024-01-25 19:44:35,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:35,539] [INFO] Task started: CheckM
[2024-01-25 19:44:35,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023077655.1_ASM2307765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023077655.1_ASM2307765v1_genomic.fna/checkm_input GCF_023077655.1_ASM2307765v1_genomic.fna/checkm_result
[2024-01-25 19:45:29,324] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:29,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 24.62%
Strain heterogeneity: 95.45%
--------------------------------------------------------------------------------
[2024-01-25 19:45:29,352] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:29,352] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:29,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023077655.1_ASM2307765v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:29,353] [INFO] Task started: Blastn
[2024-01-25 19:45:29,353] [INFO] Running command: blastn -query GCF_023077655.1_ASM2307765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35f09e0b-9ee2-4609-8fc9-a2bdedf2cf0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_023077655.1_ASM2307765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:29,861] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:29,864] [INFO] Selected 11 target genomes.
[2024-01-25 19:45:29,864] [INFO] Target genome list was writen to GCF_023077655.1_ASM2307765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:29,879] [INFO] Task started: fastANI
[2024-01-25 19:45:29,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d555171-60c1-4396-9bc5-ff566b1522f5/GCF_023077655.1_ASM2307765v1_genomic.fna.gz --refList GCF_023077655.1_ASM2307765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023077655.1_ASM2307765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:38,901] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:38,909] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:45:38,909] [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
GCA_005049285.1	s__Halorientalis sp005049285	83.7953	853	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001989615.1	s__Halorientalis sp001989615	80.5209	699	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110215.1	s__Halorientalis persicus	80.4251	695	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102305.1	s__Halorientalis regularis	80.401	660	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118325.1	s__Halorientalis sp004118325	80.3466	689	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023965.1	s__Halomicrobium mukohataei	78.4099	420	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	96.8107	100.00	100.00	1.00	1.00	4	-
GCF_004698125.1	s__Halosimplex halophilum	78.4075	536	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617995.1	s__Halomicrobium sp009617995	78.3664	435	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	95.0	97.14	97.11	0.87	0.86	3	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	78.2151	364	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-4-69-31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785955.1	s__Halostella litorea	78.026	438	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017094525.1	s__Halapricum sp017094525	77.7885	337	1526	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum	95.0	98.12	98.12	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:38,910] [INFO] GTDB search result was written to GCF_023077655.1_ASM2307765v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:38,911] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:38,913] [INFO] DFAST_QC result json was written to GCF_023077655.1_ASM2307765v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:38,913] [INFO] DFAST_QC completed!
[2024-01-25 19:45:38,913] [INFO] Total running time: 0h1m33s