[2023-06-30 11:15:56,064] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:15:56,069] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:15:56,070] [INFO] DQC Reference Directory: /var/lib/cwl/stg4513fc8d-b9c6-4422-b1df-d7a2af9a358f/dqc_reference
[2023-06-30 11:15:57,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:15:57,295] [INFO] Task started: Prodigal
[2023-06-30 11:15:57,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg51fc7f36-e047-4df3-a13f-5b2f14c01419/GCA_016784685.1_ASM1678468v1_genomic.fna.gz | prodigal -d GCA_016784685.1_ASM1678468v1_genomic.fna/cds.fna -a GCA_016784685.1_ASM1678468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:15:58,906] [INFO] Task succeeded: Prodigal
[2023-06-30 11:15:58,906] [INFO] Task started: HMMsearch
[2023-06-30 11:15:58,906] [INFO] Running command: hmmsearch --tblout GCA_016784685.1_ASM1678468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4513fc8d-b9c6-4422-b1df-d7a2af9a358f/dqc_reference/reference_markers.hmm GCA_016784685.1_ASM1678468v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:15:59,006] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:15:59,007] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg51fc7f36-e047-4df3-a13f-5b2f14c01419/GCA_016784685.1_ASM1678468v1_genomic.fna.gz]
[2023-06-30 11:15:59,023] [INFO] Query marker FASTA was written to GCA_016784685.1_ASM1678468v1_genomic.fna/markers.fasta
[2023-06-30 11:15:59,023] [INFO] Task started: Blastn
[2023-06-30 11:15:59,023] [INFO] Running command: blastn -query GCA_016784685.1_ASM1678468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4513fc8d-b9c6-4422-b1df-d7a2af9a358f/dqc_reference/reference_markers.fasta -out GCA_016784685.1_ASM1678468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:15:59,480] [INFO] Task succeeded: Blastn
[2023-06-30 11:15:59,483] [INFO] Selected 5 target genomes.
[2023-06-30 11:15:59,484] [INFO] Target genome list was writen to GCA_016784685.1_ASM1678468v1_genomic.fna/target_genomes.txt
[2023-06-30 11:15:59,485] [INFO] Task started: fastANI
[2023-06-30 11:15:59,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg51fc7f36-e047-4df3-a13f-5b2f14c01419/GCA_016784685.1_ASM1678468v1_genomic.fna.gz --refList GCA_016784685.1_ASM1678468v1_genomic.fna/target_genomes.txt --output GCA_016784685.1_ASM1678468v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:16:01,056] [INFO] Task succeeded: fastANI
[2023-06-30 11:16:01,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4513fc8d-b9c6-4422-b1df-d7a2af9a358f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:16:01,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4513fc8d-b9c6-4422-b1df-d7a2af9a358f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:16:01,062] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:16:01,063] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 11:16:01,063] [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
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	85.9831	228	271	95	below_threshold
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	85.7301	231	271	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	82.1402	191	271	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	81.8016	211	271	95	below_threshold
Nitrosopumilus piranensis	strain=D3C	GCA_000875775.1	1582439	1582439	type	True	80.8909	186	271	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 11:16:01,065] [INFO] DFAST Taxonomy check result was written to GCA_016784685.1_ASM1678468v1_genomic.fna/tc_result.tsv
[2023-06-30 11:16:01,065] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:16:01,065] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:16:01,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4513fc8d-b9c6-4422-b1df-d7a2af9a358f/dqc_reference/checkm_data
[2023-06-30 11:16:01,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:16:01,079] [INFO] Task started: CheckM
[2023-06-30 11:16:01,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016784685.1_ASM1678468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016784685.1_ASM1678468v1_genomic.fna/checkm_input GCA_016784685.1_ASM1678468v1_genomic.fna/checkm_result
[2023-06-30 11:16:13,431] [INFO] Task succeeded: CheckM
[2023-06-30 11:16:13,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:16:13,452] [INFO] ===== Completeness check finished =====
[2023-06-30 11:16:13,452] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:16:13,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016784685.1_ASM1678468v1_genomic.fna/markers.fasta)
[2023-06-30 11:16:13,453] [INFO] Task started: Blastn
[2023-06-30 11:16:13,453] [INFO] Running command: blastn -query GCA_016784685.1_ASM1678468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4513fc8d-b9c6-4422-b1df-d7a2af9a358f/dqc_reference/reference_markers_gtdb.fasta -out GCA_016784685.1_ASM1678468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:16:13,918] [INFO] Task succeeded: Blastn
[2023-06-30 11:16:13,922] [INFO] Selected 5 target genomes.
[2023-06-30 11:16:13,923] [INFO] Target genome list was writen to GCA_016784685.1_ASM1678468v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:16:13,926] [INFO] Task started: fastANI
[2023-06-30 11:16:13,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg51fc7f36-e047-4df3-a13f-5b2f14c01419/GCA_016784685.1_ASM1678468v1_genomic.fna.gz --refList GCA_016784685.1_ASM1678468v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016784685.1_ASM1678468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:16:15,388] [INFO] Task succeeded: fastANI
[2023-06-30 11:16:15,394] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 11:16:15,395] [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_014384555.1	s__Nitrosopumilus sp014384555	99.3831	236	271	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.46	99.38	0.88	0.87	3	conclusive
GCF_000299395.1	s__Nitrosopumilus sediminis	86.508	228	271	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407145.1	s__Nitrosopumilus cobalaminigenes	85.7301	231	271	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203245.1	s__Nitrosopumilus sp013203245	85.3136	193	271	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043295.1	s__Nitrosopumilus sp013043295	84.1798	167	271	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-30 11:16:15,397] [INFO] GTDB search result was written to GCA_016784685.1_ASM1678468v1_genomic.fna/result_gtdb.tsv
[2023-06-30 11:16:15,398] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:16:15,402] [INFO] DFAST_QC result json was written to GCA_016784685.1_ASM1678468v1_genomic.fna/dqc_result.json
[2023-06-30 11:16:15,402] [INFO] DFAST_QC completed!
[2023-06-30 11:16:15,402] [INFO] Total running time: 0h0m19s