[2023-06-13 18:27:47,865] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:27:47,868] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:27:47,868] [INFO] DQC Reference Directory: /var/lib/cwl/stgab41a691-1b6e-4abf-afae-00e04c2a5833/dqc_reference
[2023-06-13 18:27:49,098] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:27:49,099] [INFO] Task started: Prodigal
[2023-06-13 18:27:49,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg8546a330-4929-4c74-a76e-e2c69924f037/GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:27:52,185] [INFO] Task succeeded: Prodigal
[2023-06-13 18:27:52,186] [INFO] Task started: HMMsearch
[2023-06-13 18:27:52,186] [INFO] Running command: hmmsearch --tblout GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab41a691-1b6e-4abf-afae-00e04c2a5833/dqc_reference/reference_markers.hmm GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:27:52,425] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:27:52,427] [INFO] Found 6/6 markers.
[2023-06-13 18:27:52,451] [INFO] Query marker FASTA was written to GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 18:27:52,452] [INFO] Task started: Blastn
[2023-06-13 18:27:52,452] [INFO] Running command: blastn -query GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgab41a691-1b6e-4abf-afae-00e04c2a5833/dqc_reference/reference_markers.fasta -out GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:27:53,023] [INFO] Task succeeded: Blastn
[2023-06-13 18:27:53,031] [INFO] Selected 13 target genomes.
[2023-06-13 18:27:53,031] [INFO] Target genome list was writen to GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 18:27:53,033] [INFO] Task started: fastANI
[2023-06-13 18:27:53,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg8546a330-4929-4c74-a76e-e2c69924f037/GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:27:56,749] [INFO] Task succeeded: fastANI
[2023-06-13 18:27:56,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab41a691-1b6e-4abf-afae-00e04c2a5833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:27:56,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab41a691-1b6e-4abf-afae-00e04c2a5833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:27:56,762] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:27:56,762] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 18:27:56,762] [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 turcicus	strain=Faydin-H70	GCA_019711685.1	2867412	2867412	type	True	77.9478	138	598	95	below_threshold
Helicobacter winghamensis	strain=ATCC BAA-430	GCA_000158455.1	157268	157268	type	True	77.8703	142	598	95	below_threshold
Helicobacter pullorum	strain=CCUG 33837	GCA_017979475.1	35818	35818	type	True	77.7967	172	598	95	below_threshold
Helicobacter canadensis	strain=MIT 98-5491	GCA_000162575.1	123841	123841	type	True	77.7868	175	598	95	below_threshold
Helicobacter rodentium	strain=ATCC 700285	GCA_000687535.1	59617	59617	type	True	77.7123	139	598	95	below_threshold
Helicobacter canadensis	strain=MIT 98-5491	GCA_000155455.1	123841	123841	type	True	77.6405	173	598	95	below_threshold
Helicobacter valdiviensis	strain=WBE14	GCA_003245365.1	1458358	1458358	type	True	77.6201	175	598	95	below_threshold
Helicobacter burdigaliensis	strain=CNRCH 2005/566H	GCA_003670295.1	2315334	2315334	type	True	77.38	160	598	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:27:56,764] [INFO] DFAST Taxonomy check result was written to GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 18:27:56,765] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:27:56,765] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:27:56,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab41a691-1b6e-4abf-afae-00e04c2a5833/dqc_reference/checkm_data
[2023-06-13 18:27:56,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:27:56,792] [INFO] Task started: CheckM
[2023-06-13 18:27:56,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 18:28:13,785] [INFO] Task succeeded: CheckM
[2023-06-13 18:28:13,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:28:13,811] [INFO] ===== Completeness check finished =====
[2023-06-13 18:28:13,812] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:28:13,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 18:28:13,813] [INFO] Task started: Blastn
[2023-06-13 18:28:13,813] [INFO] Running command: blastn -query GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgab41a691-1b6e-4abf-afae-00e04c2a5833/dqc_reference/reference_markers_gtdb.fasta -out GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:28:14,606] [INFO] Task succeeded: Blastn
[2023-06-13 18:28:14,610] [INFO] Selected 15 target genomes.
[2023-06-13 18:28:14,611] [INFO] Target genome list was writen to GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:28:14,615] [INFO] Task started: fastANI
[2023-06-13 18:28:14,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg8546a330-4929-4c74-a76e-e2c69924f037/GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:28:19,556] [INFO] Task succeeded: fastANI
[2023-06-13 18:28:19,578] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 18:28:19,579] [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_000765745.2	s__Helicobacter_D apodemus	99.72	579	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	98.27	97.09	0.93	0.91	3	conclusive
GCF_900198605.1	s__Helicobacter_D mesocricetorum	86.302	470	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003364315.1	s__Helicobacter_D ganmani	78.521	143	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	99.45	99.17	0.96	0.93	4	-
GCF_000158455.1	s__Helicobacter_D winghamensis	77.8691	142	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	99.73	99.12	0.98	0.96	8	-
GCF_008801855.1	s__Helicobacter_D pullorum	77.7949	184	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	97.98	97.63	0.93	0.87	29	-
GCF_000162575.1	s__Helicobacter_D canadensis	77.7584	174	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	99.98	99.92	1.00	0.99	5	-
GCF_000687535.1	s__Helicobacter_D rodentium	77.7123	139	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	98.53	98.53	0.90	0.90	2	-
GCA_014799995.1	s__Helicobacter_D sp014799995	77.6577	133	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003245365.1	s__Helicobacter_D valdiviensis	77.6557	173	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003288905.1	s__Helicobacter_D sp003288905	77.5733	155	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000765695.2	s__Helicobacter_D sp000765695	77.4585	157	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003670295.1	s__Helicobacter_D burdigaliensis	77.4173	158	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 18:28:19,581] [INFO] GTDB search result was written to GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 18:28:19,581] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:28:19,585] [INFO] DFAST_QC result json was written to GCA_947073705.1_SRR12464015_bin.6_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 18:28:19,585] [INFO] DFAST_QC completed!
[2023-06-13 18:28:19,585] [INFO] Total running time: 0h0m32s