[2024-01-24 13:41:25,737] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg26f475f7-fcfd-4095-8e58-12ea52db3db2/dqc_reference
[2024-01-24 13:41:27,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,111] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bc35939-e6ee-43d8-9a7a-8ed3e654ffbf/GCF_009900715.1_ASM990071v1_genomic.fna.gz | prodigal -d GCF_009900715.1_ASM990071v1_genomic.fna/cds.fna -a GCF_009900715.1_ASM990071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:45,055] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:45,056] [INFO] Task started: HMMsearch
[2024-01-24 13:41:45,056] [INFO] Running command: hmmsearch --tblout GCF_009900715.1_ASM990071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26f475f7-fcfd-4095-8e58-12ea52db3db2/dqc_reference/reference_markers.hmm GCF_009900715.1_ASM990071v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:45,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:45,285] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8bc35939-e6ee-43d8-9a7a-8ed3e654ffbf/GCF_009900715.1_ASM990071v1_genomic.fna.gz]
[2024-01-24 13:41:45,314] [INFO] Query marker FASTA was written to GCF_009900715.1_ASM990071v1_genomic.fna/markers.fasta
[2024-01-24 13:41:45,315] [INFO] Task started: Blastn
[2024-01-24 13:41:45,315] [INFO] Running command: blastn -query GCF_009900715.1_ASM990071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26f475f7-fcfd-4095-8e58-12ea52db3db2/dqc_reference/reference_markers.fasta -out GCF_009900715.1_ASM990071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:45,868] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:45,871] [INFO] Selected 8 target genomes.
[2024-01-24 13:41:45,871] [INFO] Target genome list was writen to GCF_009900715.1_ASM990071v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:45,875] [INFO] Task started: fastANI
[2024-01-24 13:41:45,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc35939-e6ee-43d8-9a7a-8ed3e654ffbf/GCF_009900715.1_ASM990071v1_genomic.fna.gz --refList GCF_009900715.1_ASM990071v1_genomic.fna/target_genomes.txt --output GCF_009900715.1_ASM990071v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:52,311] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:52,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26f475f7-fcfd-4095-8e58-12ea52db3db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:52,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26f475f7-fcfd-4095-8e58-12ea52db3db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:52,321] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:52,321] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:52,321] [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
Halococcus salsus	strain=ZJ1	GCA_009900715.1	2162894	2162894	type	True	100.0	1161	1161	95	conclusive
Halococcus hamelinensis	strain=100A6	GCA_000336675.1	332168	332168	type	True	92.4346	864	1161	95	below_threshold
Halococcus hamelinensis	strain=100A6	GCA_000259215.1	332168	332168	type	True	92.2639	763	1161	95	below_threshold
Halococcus morrhuae	strain=DSM 1307	GCA_000336695.1	2250	2250	type	True	80.3275	520	1161	95	below_threshold
Halococcus qingdaonensis	strain=CGMCC 1.4243	GCA_024508235.1	224402	224402	type	True	80.1375	536	1161	95	below_threshold
Halococcus saccharolyticus	strain=DSM 5350	GCA_000336915.1	62319	62319	type	True	79.9378	532	1161	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	77.183	382	1161	95	below_threshold
Halorientalis litorea	strain=ZY14	GCA_023028225.1	2931977	2931977	type	True	76.9633	243	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:52,323] [INFO] DFAST Taxonomy check result was written to GCF_009900715.1_ASM990071v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:52,324] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:52,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:52,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26f475f7-fcfd-4095-8e58-12ea52db3db2/dqc_reference/checkm_data
[2024-01-24 13:41:52,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:52,363] [INFO] Task started: CheckM
[2024-01-24 13:41:52,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009900715.1_ASM990071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009900715.1_ASM990071v1_genomic.fna/checkm_input GCF_009900715.1_ASM990071v1_genomic.fna/checkm_result
[2024-01-24 13:42:39,068] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:39,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:39,087] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:39,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:39,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009900715.1_ASM990071v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:39,088] [INFO] Task started: Blastn
[2024-01-24 13:42:39,088] [INFO] Running command: blastn -query GCF_009900715.1_ASM990071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26f475f7-fcfd-4095-8e58-12ea52db3db2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009900715.1_ASM990071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:39,560] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:39,564] [INFO] Selected 9 target genomes.
[2024-01-24 13:42:39,564] [INFO] Target genome list was writen to GCF_009900715.1_ASM990071v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:39,580] [INFO] Task started: fastANI
[2024-01-24 13:42:39,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc35939-e6ee-43d8-9a7a-8ed3e654ffbf/GCF_009900715.1_ASM990071v1_genomic.fna.gz --refList GCF_009900715.1_ASM990071v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009900715.1_ASM990071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:47,314] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:47,323] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:47,323] [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_009900715.1	s__Halococcus salsus	100.0	1161	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	95.85	95.85	0.78	0.78	2	conclusive
GCF_000336675.1	s__Halococcus hamelinensis	92.455	863	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_000336695.1	s__Halococcus morrhuae	80.3175	521	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000334895.1	s__Halococcus agarilyticus	80.1386	586	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000755245.1	s__Halococcus sediminicola	80.069	584	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336915.1	s__Halococcus saccharolyticus	79.9005	535	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004698125.1	s__Halosimplex halophilum	77.1899	382	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017094525.1	s__Halapricum sp017094525	76.9695	209	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum	95.0	98.12	98.12	0.88	0.88	2	-
GCA_003021235.1	s__Halococcus sp003021235	76.9583	277	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:47,325] [INFO] GTDB search result was written to GCF_009900715.1_ASM990071v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:47,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:47,329] [INFO] DFAST_QC result json was written to GCF_009900715.1_ASM990071v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:47,330] [INFO] DFAST_QC completed!
[2024-01-24 13:42:47,330] [INFO] Total running time: 0h1m22s