[2024-01-24 10:47:06,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg134286c4-33da-4bd2-85ca-61fe2a1681ea/dqc_reference
[2024-01-24 10:47:12,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,818] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg8261021a-70db-407a-8ff7-002b43f36e62/GCF_026000295.1_ASM2600029v1_genomic.fna.gz | prodigal -d GCF_026000295.1_ASM2600029v1_genomic.fna/cds.fna -a GCF_026000295.1_ASM2600029v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:16,797] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:16,797] [INFO] Task started: HMMsearch
[2024-01-24 10:47:16,797] [INFO] Running command: hmmsearch --tblout GCF_026000295.1_ASM2600029v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg134286c4-33da-4bd2-85ca-61fe2a1681ea/dqc_reference/reference_markers.hmm GCF_026000295.1_ASM2600029v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:17,049] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:17,051] [INFO] Found 6/6 markers.
[2024-01-24 10:47:17,098] [INFO] Query marker FASTA was written to GCF_026000295.1_ASM2600029v1_genomic.fna/markers.fasta
[2024-01-24 10:47:17,099] [INFO] Task started: Blastn
[2024-01-24 10:47:17,099] [INFO] Running command: blastn -query GCF_026000295.1_ASM2600029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg134286c4-33da-4bd2-85ca-61fe2a1681ea/dqc_reference/reference_markers.fasta -out GCF_026000295.1_ASM2600029v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,608] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,611] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:19,612] [INFO] Target genome list was writen to GCF_026000295.1_ASM2600029v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:20,433] [INFO] Task started: fastANI
[2024-01-24 10:47:20,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg8261021a-70db-407a-8ff7-002b43f36e62/GCF_026000295.1_ASM2600029v1_genomic.fna.gz --refList GCF_026000295.1_ASM2600029v1_genomic.fna/target_genomes.txt --output GCF_026000295.1_ASM2600029v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:23,842] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:23,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg134286c4-33da-4bd2-85ca-61fe2a1681ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:23,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg134286c4-33da-4bd2-85ca-61fe2a1681ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:24,177] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:24,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:24,177] [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
Helicobacter suis	strain=DSM 19735	GCA_017979375.1	104628	104628	type	True	99.7429	489	591	95	conclusive
Helicobacter suis	strain=HS1	GCA_000187625.2	104628	104628	type	True	99.6976	494	591	95	conclusive
Helicobacter ailurogastricus		GCA_001282945.1	1578720	1578720	type	True	77.8574	128	591	95	below_threshold
Helicobacter heilmannii		GCA_001283065.1	35817	35817	type	True	77.6524	104	591	95	below_threshold
Helicobacter heilmannii	strain=LMG 26292	GCA_017979395.1	35817	35817	type	True	77.3779	100	591	95	below_threshold
Helicobacter salomonis	strain=CIP 105607	GCA_017979425.1	56878	56878	type	True	77.3191	103	591	95	below_threshold
Helicobacter mehlei	strain=L15	GCA_003660265.1	2316080	2316080	type	True	77.1557	177	591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:24,179] [INFO] DFAST Taxonomy check result was written to GCF_026000295.1_ASM2600029v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:24,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:24,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:24,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg134286c4-33da-4bd2-85ca-61fe2a1681ea/dqc_reference/checkm_data
[2024-01-24 10:47:24,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:24,208] [INFO] Task started: CheckM
[2024-01-24 10:47:24,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026000295.1_ASM2600029v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026000295.1_ASM2600029v1_genomic.fna/checkm_input GCF_026000295.1_ASM2600029v1_genomic.fna/checkm_result
[2024-01-24 10:47:44,867] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:44,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:44,888] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:44,889] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:44,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026000295.1_ASM2600029v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:44,890] [INFO] Task started: Blastn
[2024-01-24 10:47:44,890] [INFO] Running command: blastn -query GCF_026000295.1_ASM2600029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg134286c4-33da-4bd2-85ca-61fe2a1681ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_026000295.1_ASM2600029v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:47,668] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:47,672] [INFO] Selected 9 target genomes.
[2024-01-24 10:47:47,673] [INFO] Target genome list was writen to GCF_026000295.1_ASM2600029v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:47,822] [INFO] Task started: fastANI
[2024-01-24 10:47:47,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg8261021a-70db-407a-8ff7-002b43f36e62/GCF_026000295.1_ASM2600029v1_genomic.fna.gz --refList GCF_026000295.1_ASM2600029v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026000295.1_ASM2600029v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:47:51,669] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:51,687] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:47:51,687] [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_000187625.1	s__Helicobacter_E suis	99.6976	494	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	99.74	99.56	0.96	0.89	27	conclusive
GCF_902196135.1	s__Helicobacter_E suis_A	93.3028	495	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	97.68	97.34	0.95	0.91	4	-
GCF_902196125.1	s__Helicobacter_E suis_B	91.5515	480	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	96.42	96.42	0.94	0.90	3	-
GCF_000259255.1	s__Helicobacter cetorum_B	78.8431	65	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0	96.46	95.82	0.94	0.93	3	-
GCF_900197855.1	s__Helicobacter_E cynogastricus	77.8581	125	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282945.1	s__Helicobacter_E ailurogastricus	77.8574	128	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.41	98.32	0.95	0.92	6	-
GCF_001283065.1	s__Helicobacter_E heilmannii	77.6839	103	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.65	98.18	0.97	0.95	9	-
GCF_017979425.1	s__Helicobacter_E salomonis	77.29	106	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.86	98.52	0.94	0.92	6	-
GCF_003660265.1	s__Helicobacter_E mehlei	77.1857	175	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	99.56	99.56	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:47:51,695] [INFO] GTDB search result was written to GCF_026000295.1_ASM2600029v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:47:51,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:47:51,699] [INFO] DFAST_QC result json was written to GCF_026000295.1_ASM2600029v1_genomic.fna/dqc_result.json
[2024-01-24 10:47:51,699] [INFO] DFAST_QC completed!
[2024-01-24 10:47:51,699] [INFO] Total running time: 0h0m45s