[2024-01-24 13:57:13,145] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b474474-269b-4dc8-bc25-56cbb4382bdf/dqc_reference
[2024-01-24 13:57:14,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,520] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,520] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4fa1b06-c78f-4463-b87f-bc8fedabbf85/GCF_009184545.1_ASM918454v1_genomic.fna.gz | prodigal -d GCF_009184545.1_ASM918454v1_genomic.fna/cds.fna -a GCF_009184545.1_ASM918454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:28,605] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:28,605] [INFO] Task started: HMMsearch
[2024-01-24 13:57:28,605] [INFO] Running command: hmmsearch --tblout GCF_009184545.1_ASM918454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b474474-269b-4dc8-bc25-56cbb4382bdf/dqc_reference/reference_markers.hmm GCF_009184545.1_ASM918454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:28,847] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:28,848] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf4fa1b06-c78f-4463-b87f-bc8fedabbf85/GCF_009184545.1_ASM918454v1_genomic.fna.gz]
[2024-01-24 13:57:28,875] [INFO] Query marker FASTA was written to GCF_009184545.1_ASM918454v1_genomic.fna/markers.fasta
[2024-01-24 13:57:28,875] [INFO] Task started: Blastn
[2024-01-24 13:57:28,875] [INFO] Running command: blastn -query GCF_009184545.1_ASM918454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b474474-269b-4dc8-bc25-56cbb4382bdf/dqc_reference/reference_markers.fasta -out GCF_009184545.1_ASM918454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:29,406] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:29,409] [INFO] Selected 9 target genomes.
[2024-01-24 13:57:29,409] [INFO] Target genome list was writen to GCF_009184545.1_ASM918454v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:29,416] [INFO] Task started: fastANI
[2024-01-24 13:57:29,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4fa1b06-c78f-4463-b87f-bc8fedabbf85/GCF_009184545.1_ASM918454v1_genomic.fna.gz --refList GCF_009184545.1_ASM918454v1_genomic.fna/target_genomes.txt --output GCF_009184545.1_ASM918454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:36,380] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:36,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b474474-269b-4dc8-bc25-56cbb4382bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:36,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b474474-269b-4dc8-bc25-56cbb4382bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:36,390] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:36,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:36,391] [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
Halosegnis rubeus	strain=F17-44	GCA_009184545.1	2212850	2212850	type	True	100.0	880	882	95	conclusive
Halosegnis longus	strain=F12-1	GCA_009663395.1	2216012	2216012	type	True	91.5681	698	882	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	78.5027	347	882	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	78.1074	329	882	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	78.0166	340	882	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000337315.1	2246	2246	type	True	77.9867	321	882	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	77.6061	320	882	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	77.3465	318	882	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	77.2256	274	882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:36,392] [INFO] DFAST Taxonomy check result was written to GCF_009184545.1_ASM918454v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:36,393] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:36,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:36,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b474474-269b-4dc8-bc25-56cbb4382bdf/dqc_reference/checkm_data
[2024-01-24 13:57:36,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:36,426] [INFO] Task started: CheckM
[2024-01-24 13:57:36,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009184545.1_ASM918454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009184545.1_ASM918454v1_genomic.fna/checkm_input GCF_009184545.1_ASM918454v1_genomic.fna/checkm_result
[2024-01-24 13:58:20,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:20,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:20,952] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:20,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:20,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009184545.1_ASM918454v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:20,953] [INFO] Task started: Blastn
[2024-01-24 13:58:20,953] [INFO] Running command: blastn -query GCF_009184545.1_ASM918454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b474474-269b-4dc8-bc25-56cbb4382bdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_009184545.1_ASM918454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:21,455] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:21,458] [INFO] Selected 7 target genomes.
[2024-01-24 13:58:21,458] [INFO] Target genome list was writen to GCF_009184545.1_ASM918454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:21,472] [INFO] Task started: fastANI
[2024-01-24 13:58:21,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4fa1b06-c78f-4463-b87f-bc8fedabbf85/GCF_009184545.1_ASM918454v1_genomic.fna.gz --refList GCF_009184545.1_ASM918454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009184545.1_ASM918454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:25,839] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:25,847] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:25,847] [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_009184545.1	s__CBA1134 sp009184545	100.0	880	882	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	99.60	99.56	0.94	0.94	3	conclusive
GCF_001950595.1	s__CBA1134 sp001950595	91.6091	696	882	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	99.03	98.86	0.91	0.88	3	-
GCA_003021785.1	s__CBA1134 sp003021785	83.8242	558	882	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	97.75	97.59	0.93	0.92	3	-
GCA_003023185.1	s__CBA1134 sp003023185	80.0324	343	882	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021175.1	s__CBA1134 sp003021175	80.023	440	882	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	78.0228	340	882	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021005.1	s__Natronomonas sp003021005	77.215	197	882	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 13:58:25,849] [INFO] GTDB search result was written to GCF_009184545.1_ASM918454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:25,850] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:25,854] [INFO] DFAST_QC result json was written to GCF_009184545.1_ASM918454v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:25,854] [INFO] DFAST_QC completed!
[2024-01-24 13:58:25,855] [INFO] Total running time: 0h1m13s