[2024-01-25 19:50:35,821] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:35,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:35,822] [INFO] DQC Reference Directory: /var/lib/cwl/stg76230a26-f86e-430f-901e-cd1bf56623ed/dqc_reference
[2024-01-25 19:50:37,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:37,001] [INFO] Task started: Prodigal
[2024-01-25 19:50:37,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d06f1ce-9bf4-42a9-9879-30740cf48b6b/GCF_023699475.1_ASM2369947v1_genomic.fna.gz | prodigal -d GCF_023699475.1_ASM2369947v1_genomic.fna/cds.fna -a GCF_023699475.1_ASM2369947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:54,732] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:54,732] [INFO] Task started: HMMsearch
[2024-01-25 19:50:54,732] [INFO] Running command: hmmsearch --tblout GCF_023699475.1_ASM2369947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76230a26-f86e-430f-901e-cd1bf56623ed/dqc_reference/reference_markers.hmm GCF_023699475.1_ASM2369947v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:54,951] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:54,952] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2d06f1ce-9bf4-42a9-9879-30740cf48b6b/GCF_023699475.1_ASM2369947v1_genomic.fna.gz]
[2024-01-25 19:50:54,996] [INFO] Query marker FASTA was written to GCF_023699475.1_ASM2369947v1_genomic.fna/markers.fasta
[2024-01-25 19:50:54,996] [INFO] Task started: Blastn
[2024-01-25 19:50:54,996] [INFO] Running command: blastn -query GCF_023699475.1_ASM2369947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76230a26-f86e-430f-901e-cd1bf56623ed/dqc_reference/reference_markers.fasta -out GCF_023699475.1_ASM2369947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:55,528] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:55,531] [INFO] Selected 8 target genomes.
[2024-01-25 19:50:55,531] [INFO] Target genome list was writen to GCF_023699475.1_ASM2369947v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:55,538] [INFO] Task started: fastANI
[2024-01-25 19:50:55,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d06f1ce-9bf4-42a9-9879-30740cf48b6b/GCF_023699475.1_ASM2369947v1_genomic.fna.gz --refList GCF_023699475.1_ASM2369947v1_genomic.fna/target_genomes.txt --output GCF_023699475.1_ASM2369947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:03,358] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:03,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76230a26-f86e-430f-901e-cd1bf56623ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:03,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76230a26-f86e-430f-901e-cd1bf56623ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:03,369] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:03,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:03,370] [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
Halomarina rubra	strain=ZS-47-S	GCA_023699475.1	2071873	2071873	type	True	100.0	1347	1347	95	conclusive
Halomarina oriensis	strain=JCM 16495	GCA_009791395.1	671145	671145	type	True	86.0071	918	1347	95	below_threshold
Halomarina salina	strain=ZS-57-S	GCA_023074835.1	1872699	1872699	type	True	85.1089	931	1347	95	below_threshold
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	78.0689	482	1347	95	below_threshold
Halostella salina	strain=CBA1114	GCA_003675855.1	1547897	1547897	type	True	78.0276	450	1347	95	below_threshold
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	78.0205	510	1347	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	77.9368	485	1347	95	below_threshold
Halorussus halobius	strain=HD8-83	GCA_004765805.1	1710537	1710537	type	True	77.7332	453	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:03,372] [INFO] DFAST Taxonomy check result was written to GCF_023699475.1_ASM2369947v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:03,373] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:03,373] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:03,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76230a26-f86e-430f-901e-cd1bf56623ed/dqc_reference/checkm_data
[2024-01-25 19:51:03,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:03,418] [INFO] Task started: CheckM
[2024-01-25 19:51:03,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023699475.1_ASM2369947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023699475.1_ASM2369947v1_genomic.fna/checkm_input GCF_023699475.1_ASM2369947v1_genomic.fna/checkm_result
[2024-01-25 19:51:51,019] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:51,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:51,044] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:51,045] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:51,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023699475.1_ASM2369947v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:51,045] [INFO] Task started: Blastn
[2024-01-25 19:51:51,045] [INFO] Running command: blastn -query GCF_023699475.1_ASM2369947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76230a26-f86e-430f-901e-cd1bf56623ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_023699475.1_ASM2369947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:51,606] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:51,610] [INFO] Selected 10 target genomes.
[2024-01-25 19:51:51,610] [INFO] Target genome list was writen to GCF_023699475.1_ASM2369947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:51,624] [INFO] Task started: fastANI
[2024-01-25 19:51:51,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d06f1ce-9bf4-42a9-9879-30740cf48b6b/GCF_023699475.1_ASM2369947v1_genomic.fna.gz --refList GCF_023699475.1_ASM2369947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023699475.1_ASM2369947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:00,285] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:00,292] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:52:00,293] [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_009791395.1	s__Halomarina oriensis	85.9714	922	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021975.1	s__Halomarina sp003021975	79.5558	507	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023565.1	s__Halostella sp003023565	78.155	417	1347	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	-
GCF_004785955.1	s__Halostella litorea	78.0883	479	1347	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	-
GCF_003675855.1	s__Halostella salina	78.0497	449	1347	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	-
GCF_900112175.1	s__Halogeometricum rufum	78.0416	506	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	-
GCF_003369835.1	s__Halorussus rarus	77.9267	499	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010119195.1	s__Haloarcula salina	77.8899	439	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004765805.1	s__Halorussus sp004765805	77.7839	447	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021325.1	s__Natronomonas sp003021325	77.4385	268	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:00,294] [INFO] GTDB search result was written to GCF_023699475.1_ASM2369947v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:00,294] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:00,297] [INFO] DFAST_QC result json was written to GCF_023699475.1_ASM2369947v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:00,297] [INFO] DFAST_QC completed!
[2024-01-25 19:52:00,297] [INFO] Total running time: 0h1m24s