[2024-01-24 12:29:19,695] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:19,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:19,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg225fbc4d-9686-4f8b-b69b-754b5be01ee5/dqc_reference
[2024-01-24 12:29:20,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:20,874] [INFO] Task started: Prodigal
[2024-01-24 12:29:20,874] [INFO] Running command: gunzip -c /var/lib/cwl/stg5623a397-d810-45f1-970b-1cf7d285c208/GCF_024298825.1_ASM2429882v1_genomic.fna.gz | prodigal -d GCF_024298825.1_ASM2429882v1_genomic.fna/cds.fna -a GCF_024298825.1_ASM2429882v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:42,540] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:42,541] [INFO] Task started: HMMsearch
[2024-01-24 12:29:42,541] [INFO] Running command: hmmsearch --tblout GCF_024298825.1_ASM2429882v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg225fbc4d-9686-4f8b-b69b-754b5be01ee5/dqc_reference/reference_markers.hmm GCF_024298825.1_ASM2429882v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:42,795] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:42,796] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5623a397-d810-45f1-970b-1cf7d285c208/GCF_024298825.1_ASM2429882v1_genomic.fna.gz]
[2024-01-24 12:29:42,833] [INFO] Query marker FASTA was written to GCF_024298825.1_ASM2429882v1_genomic.fna/markers.fasta
[2024-01-24 12:29:42,833] [INFO] Task started: Blastn
[2024-01-24 12:29:42,833] [INFO] Running command: blastn -query GCF_024298825.1_ASM2429882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg225fbc4d-9686-4f8b-b69b-754b5be01ee5/dqc_reference/reference_markers.fasta -out GCF_024298825.1_ASM2429882v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:43,360] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:43,363] [INFO] Selected 9 target genomes.
[2024-01-24 12:29:43,364] [INFO] Target genome list was writen to GCF_024298825.1_ASM2429882v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:43,372] [INFO] Task started: fastANI
[2024-01-24 12:29:43,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg5623a397-d810-45f1-970b-1cf7d285c208/GCF_024298825.1_ASM2429882v1_genomic.fna.gz --refList GCF_024298825.1_ASM2429882v1_genomic.fna/target_genomes.txt --output GCF_024298825.1_ASM2429882v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:51,285] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:51,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg225fbc4d-9686-4f8b-b69b-754b5be01ee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:51,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg225fbc4d-9686-4f8b-b69b-754b5be01ee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:51,294] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:29:51,294] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:29:51,294] [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
Haloglomus irregulare	strain=F16-60	GCA_007421925.1	2234134	2234134	type	True	83.0351	811	1396	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	78.9975	597	1396	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	78.8132	531	1396	95	below_threshold
Halomarina salina	strain=ZS-57-S	GCA_023074835.1	1872699	1872699	type	True	78.1466	492	1396	95	below_threshold
Halomarina rubra	strain=ZS-47-S	GCA_023699475.1	2071873	2071873	type	True	78.0576	448	1396	95	below_threshold
Haloarchaeobius litoreus	strain=GX1	GCA_024495425.1	755306	755306	type	True	78.0078	483	1396	95	below_threshold
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	77.8331	400	1396	95	below_threshold
Halosimplex carlsbadense	strain=2-9-1	GCA_000337455.1	171164	171164	type	True	77.8136	445	1396	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	77.6787	482	1396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:51,296] [INFO] DFAST Taxonomy check result was written to GCF_024298825.1_ASM2429882v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:51,296] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:51,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:51,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg225fbc4d-9686-4f8b-b69b-754b5be01ee5/dqc_reference/checkm_data
[2024-01-24 12:29:51,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:51,338] [INFO] Task started: CheckM
[2024-01-24 12:29:51,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024298825.1_ASM2429882v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024298825.1_ASM2429882v1_genomic.fna/checkm_input GCF_024298825.1_ASM2429882v1_genomic.fna/checkm_result
[2024-01-24 12:30:49,287] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:49,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.09%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 12:30:49,315] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:49,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:49,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024298825.1_ASM2429882v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:49,316] [INFO] Task started: Blastn
[2024-01-24 12:30:49,316] [INFO] Running command: blastn -query GCF_024298825.1_ASM2429882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg225fbc4d-9686-4f8b-b69b-754b5be01ee5/dqc_reference/reference_markers_gtdb.fasta -out GCF_024298825.1_ASM2429882v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:49,835] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:49,839] [INFO] Selected 9 target genomes.
[2024-01-24 12:30:49,839] [INFO] Target genome list was writen to GCF_024298825.1_ASM2429882v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:49,847] [INFO] Task started: fastANI
[2024-01-24 12:30:49,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg5623a397-d810-45f1-970b-1cf7d285c208/GCF_024298825.1_ASM2429882v1_genomic.fna.gz --refList GCF_024298825.1_ASM2429882v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024298825.1_ASM2429882v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:56,110] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:56,126] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:30:56,126] [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_003020985.1	s__Haloglomus sp003020985	84.3296	768	1396	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloglomus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007421925.1	s__Haloglomus irregulare	83.0392	811	1396	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloglomus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	78.7938	534	1396	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018609665.1	s__Natronomonas sp018609665	78.1813	367	1396	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022005.1	s__QS-5-70-15 sp003022005	78.114	418	1396	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-5-70-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391635.1	s__Natronomonas gomsonensis	77.9606	413	1396	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020965.1	s__Natronomonas sp003020965	77.7423	419	1396	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	77.6339	315	1396	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	-
GCA_007135435.1	s__Natronomonas sp007135435	77.5009	289	1396	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:56,133] [INFO] GTDB search result was written to GCF_024298825.1_ASM2429882v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:56,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:56,137] [INFO] DFAST_QC result json was written to GCF_024298825.1_ASM2429882v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:56,138] [INFO] DFAST_QC completed!
[2024-01-24 12:30:56,138] [INFO] Total running time: 0h1m36s