[2024-01-24 12:36:24,524] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg65ad31ad-d6e6-424a-955f-6e3648b06950/dqc_reference
[2024-01-24 12:36:25,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,817] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg00639065-3cb4-47f8-b0a3-a741278edf72/GCF_017873555.1_ASM1787355v1_genomic.fna.gz | prodigal -d GCF_017873555.1_ASM1787355v1_genomic.fna/cds.fna -a GCF_017873555.1_ASM1787355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:39,177] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:39,178] [INFO] Task started: HMMsearch
[2024-01-24 12:36:39,178] [INFO] Running command: hmmsearch --tblout GCF_017873555.1_ASM1787355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65ad31ad-d6e6-424a-955f-6e3648b06950/dqc_reference/reference_markers.hmm GCF_017873555.1_ASM1787355v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:39,405] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:39,407] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg00639065-3cb4-47f8-b0a3-a741278edf72/GCF_017873555.1_ASM1787355v1_genomic.fna.gz]
[2024-01-24 12:36:39,435] [INFO] Query marker FASTA was written to GCF_017873555.1_ASM1787355v1_genomic.fna/markers.fasta
[2024-01-24 12:36:39,435] [INFO] Task started: Blastn
[2024-01-24 12:36:39,435] [INFO] Running command: blastn -query GCF_017873555.1_ASM1787355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ad31ad-d6e6-424a-955f-6e3648b06950/dqc_reference/reference_markers.fasta -out GCF_017873555.1_ASM1787355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:39,975] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:39,980] [INFO] Selected 7 target genomes.
[2024-01-24 12:36:39,981] [INFO] Target genome list was writen to GCF_017873555.1_ASM1787355v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:39,985] [INFO] Task started: fastANI
[2024-01-24 12:36:39,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg00639065-3cb4-47f8-b0a3-a741278edf72/GCF_017873555.1_ASM1787355v1_genomic.fna.gz --refList GCF_017873555.1_ASM1787355v1_genomic.fna/target_genomes.txt --output GCF_017873555.1_ASM1787355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:47,589] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:47,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65ad31ad-d6e6-424a-955f-6e3648b06950/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:47,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65ad31ad-d6e6-424a-955f-6e3648b06950/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:47,603] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:36:47,603] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:36:47,603] [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
Halorubrum distributum	strain=JCM 10118	GCA_000337335.1	29283	29283	suspected-type	True	90.6692	766	1011	95	below_threshold
Halorubrum distributum	strain=JCM 9100	GCA_000337055.1	29283	29283	suspected-type	True	90.6488	766	1011	95	below_threshold
Halorubrum arcis	strain=JCM 13916	GCA_000337015.1	368454	368454	type	True	90.5917	760	1011	95	below_threshold
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	89.4458	742	1011	95	below_threshold
Halorubrum ezzemoulense	strain=DSM 17463	GCA_000421805.1	337243	337243	type	True	89.1932	770	1011	95	below_threshold
Halorubrum ezzemoulense	strain=DSM 17463	GCA_002114285.1	337243	337243	type	True	89.1649	729	1011	95	below_threshold
Halorubrum depositum	strain=Y78	GCA_007671725.1	2583992	2583992	type	True	86.146	721	1011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:47,605] [INFO] DFAST Taxonomy check result was written to GCF_017873555.1_ASM1787355v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:47,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:47,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:47,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65ad31ad-d6e6-424a-955f-6e3648b06950/dqc_reference/checkm_data
[2024-01-24 12:36:47,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:47,642] [INFO] Task started: CheckM
[2024-01-24 12:36:47,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873555.1_ASM1787355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873555.1_ASM1787355v1_genomic.fna/checkm_input GCF_017873555.1_ASM1787355v1_genomic.fna/checkm_result
[2024-01-24 12:37:26,649] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:26,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:26,668] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:26,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:26,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873555.1_ASM1787355v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:26,670] [INFO] Task started: Blastn
[2024-01-24 12:37:26,670] [INFO] Running command: blastn -query GCF_017873555.1_ASM1787355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ad31ad-d6e6-424a-955f-6e3648b06950/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873555.1_ASM1787355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:27,203] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:27,207] [INFO] Selected 10 target genomes.
[2024-01-24 12:37:27,208] [INFO] Target genome list was writen to GCF_017873555.1_ASM1787355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:27,217] [INFO] Task started: fastANI
[2024-01-24 12:37:27,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg00639065-3cb4-47f8-b0a3-a741278edf72/GCF_017873555.1_ASM1787355v1_genomic.fna.gz --refList GCF_017873555.1_ASM1787355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873555.1_ASM1787355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:38,632] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:38,647] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:38,647] [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_017873555.1	s__Halorubrum trapanicum	100.0	1010	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018623055.1	s__Halorubrum sp018623055	91.2726	764	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337335.1	s__Halorubrum distributum	90.6705	765	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.52	97.80	0.88	0.83	7	-
GCF_900102375.1	s__Halorubrum xinjiangense	90.5405	789	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666015.1	s__Halorubrum sp003666015	90.3022	804	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111935.1	s__Halorubrum sodomense	90.2577	761	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.32	99.30	0.92	0.90	3	-
GCF_000336875.1	s__Halorubrum californiense	89.8479	775	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.69	99.69	0.88	0.88	2	-
GCF_000337035.1	s__Halorubrum coriense	89.4457	742	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002114285.1	s__Halorubrum ezzemoulense	89.185	728	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.69	98.29	0.85	0.81	17	-
GCF_004114375.1	s__Halorubrum sp004114375	89.0522	760	1011	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:38,649] [INFO] GTDB search result was written to GCF_017873555.1_ASM1787355v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:38,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:38,653] [INFO] DFAST_QC result json was written to GCF_017873555.1_ASM1787355v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:38,653] [INFO] DFAST_QC completed!
[2024-01-24 12:37:38,653] [INFO] Total running time: 0h1m14s