[2024-01-24 13:28:54,933] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:54,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:54,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg17d4cd63-810a-42d0-8918-154890ecdf0b/dqc_reference
[2024-01-24 13:28:56,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:56,131] [INFO] Task started: Prodigal
[2024-01-24 13:28:56,132] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ec1802f-fc46-465c-a6d1-332a860b1297/GCF_000686565.1_ASM68656v1_genomic.fna.gz | prodigal -d GCF_000686565.1_ASM68656v1_genomic.fna/cds.fna -a GCF_000686565.1_ASM68656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:29:00,834] [INFO] Task succeeded: Prodigal
[2024-01-24 13:29:00,835] [INFO] Task started: HMMsearch
[2024-01-24 13:29:00,835] [INFO] Running command: hmmsearch --tblout GCF_000686565.1_ASM68656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17d4cd63-810a-42d0-8918-154890ecdf0b/dqc_reference/reference_markers.hmm GCF_000686565.1_ASM68656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:29:01,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:29:01,096] [INFO] Found 6/6 markers.
[2024-01-24 13:29:01,121] [INFO] Query marker FASTA was written to GCF_000686565.1_ASM68656v1_genomic.fna/markers.fasta
[2024-01-24 13:29:01,122] [INFO] Task started: Blastn
[2024-01-24 13:29:01,122] [INFO] Running command: blastn -query GCF_000686565.1_ASM68656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17d4cd63-810a-42d0-8918-154890ecdf0b/dqc_reference/reference_markers.fasta -out GCF_000686565.1_ASM68656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:01,705] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:01,708] [INFO] Selected 11 target genomes.
[2024-01-24 13:29:01,708] [INFO] Target genome list was writen to GCF_000686565.1_ASM68656v1_genomic.fna/target_genomes.txt
[2024-01-24 13:29:01,757] [INFO] Task started: fastANI
[2024-01-24 13:29:01,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ec1802f-fc46-465c-a6d1-332a860b1297/GCF_000686565.1_ASM68656v1_genomic.fna.gz --refList GCF_000686565.1_ASM68656v1_genomic.fna/target_genomes.txt --output GCF_000686565.1_ASM68656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:07,029] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:07,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17d4cd63-810a-42d0-8918-154890ecdf0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:07,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17d4cd63-810a-42d0-8918-154890ecdf0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:07,043] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:07,044] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:07,044] [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 bilis	strain=ATCC 51630	GCA_000686565.1	37372	37372	type	True	100.0	747	759	95	conclusive
Helicobacter bilis	strain=ATCC 51630	GCA_000765785.2	37372	37372	type	True	99.9752	713	759	95	conclusive
Helicobacter trogontum	strain=ATCC 700114	GCA_000765905.2	50960	50960	type	True	82.3255	502	759	95	below_threshold
Helicobacter himalayensis	strain=YS1	GCA_001602095.1	1591088	1591088	type	True	78.2207	54	759	95	below_threshold
Helicobacter aurati	strain=MIT 97-5075	GCA_003364265.1	137778	137778	type	True	76.9757	76	759	95	below_threshold
Helicobacter didelphidarum	strain=MIT 17-337	GCA_003364195.1	2040648	2040648	type	True	76.9356	144	759	95	below_threshold
Helicobacter jaachi	strain=MIT 09-6949	GCA_000763135.2	1677920	1677920	type	True	76.8892	52	759	95	below_threshold
Helicobacter saguini	strain=MIT 97-6194	GCA_000762875.2	1548018	1548018	type	True	76.3015	127	759	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:07,045] [INFO] DFAST Taxonomy check result was written to GCF_000686565.1_ASM68656v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:07,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:07,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:07,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17d4cd63-810a-42d0-8918-154890ecdf0b/dqc_reference/checkm_data
[2024-01-24 13:29:07,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:07,073] [INFO] Task started: CheckM
[2024-01-24 13:29:07,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000686565.1_ASM68656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000686565.1_ASM68656v1_genomic.fna/checkm_input GCF_000686565.1_ASM68656v1_genomic.fna/checkm_result
[2024-01-24 13:29:29,383] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:29,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:29,400] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:29,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:29,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000686565.1_ASM68656v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:29,401] [INFO] Task started: Blastn
[2024-01-24 13:29:29,401] [INFO] Running command: blastn -query GCF_000686565.1_ASM68656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17d4cd63-810a-42d0-8918-154890ecdf0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000686565.1_ASM68656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:30,195] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:30,198] [INFO] Selected 5 target genomes.
[2024-01-24 13:29:30,198] [INFO] Target genome list was writen to GCF_000686565.1_ASM68656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:30,253] [INFO] Task started: fastANI
[2024-01-24 13:29:30,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ec1802f-fc46-465c-a6d1-332a860b1297/GCF_000686565.1_ASM68656v1_genomic.fna.gz --refList GCF_000686565.1_ASM68656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000686565.1_ASM68656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:34,199] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:34,205] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:34,205] [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_000686565.1	s__Helicobacter_A bilis	100.0	747	759	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	96.5798	99.95	99.91	0.97	0.95	5	conclusive
GCF_900198625.1	s__Helicobacter_A rappini	96.4434	677	759	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	96.5798	99.06	97.29	0.97	0.92	4	-
GCF_001999985.1	s__Helicobacter_A bilis_A	95.3818	628	759	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	96.3516	N/A	N/A	N/A	N/A	1	-
GCF_900198365.1	s__Helicobacter_A bilis_B	94.5903	590	759	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	95.8327	99.79	99.65	0.98	0.97	3	-
GCF_000765905.2	s__Helicobacter_A trogontum	82.301	504	759	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	95.0	97.76	97.01	0.91	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:34,208] [INFO] GTDB search result was written to GCF_000686565.1_ASM68656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:34,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:34,211] [INFO] DFAST_QC result json was written to GCF_000686565.1_ASM68656v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:34,211] [INFO] DFAST_QC completed!
[2024-01-24 13:29:34,211] [INFO] Total running time: 0h0m39s