[2024-01-25 20:19:35,512] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:35,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:35,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b64130c-59cf-4253-99aa-0ad34ffab983/dqc_reference
[2024-01-25 20:19:36,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:36,647] [INFO] Task started: Prodigal
[2024-01-25 20:19:36,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg8928e6a4-738a-43cd-a56a-9e29edce67cb/GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/cds.fna -a GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:57,748] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:57,748] [INFO] Task started: HMMsearch
[2024-01-25 20:19:57,748] [INFO] Running command: hmmsearch --tblout GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b64130c-59cf-4253-99aa-0ad34ffab983/dqc_reference/reference_markers.hmm GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:57,999] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:58,000] [INFO] Found 6/6 markers.
[2024-01-25 20:19:58,038] [INFO] Query marker FASTA was written to GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:19:58,039] [INFO] Task started: Blastn
[2024-01-25 20:19:58,039] [INFO] Running command: blastn -query GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b64130c-59cf-4253-99aa-0ad34ffab983/dqc_reference/reference_markers.fasta -out GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:58,630] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:58,632] [INFO] Selected 10 target genomes.
[2024-01-25 20:19:58,632] [INFO] Target genome list was writen to GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:19:58,646] [INFO] Task started: fastANI
[2024-01-25 20:19:58,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg8928e6a4-738a-43cd-a56a-9e29edce67cb/GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna.gz --refList GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:09,316] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:09,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b64130c-59cf-4253-99aa-0ad34ffab983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:09,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b64130c-59cf-4253-99aa-0ad34ffab983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:09,324] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:09,324] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:09,324] [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
Pontibacter indicus	strain=LP100	GCA_900156345.1	1317125	1317125	type	True	100.0	1517	1518	95	conclusive
Pontibacter amylolyticus	strain=CGMCC 1.12749	GCA_014638845.1	1424080	1424080	type	True	85.8298	1273	1518	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	84.7398	1179	1518	95	below_threshold
Pontibacter virosus	strain=DSM 100231	GCA_003096355.1	1765052	1765052	type	True	84.2528	1180	1518	95	below_threshold
Pontibacter lucknowensis	strain=DM9	GCA_900156415.1	1077936	1077936	type	True	83.0569	1143	1518	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	81.0036	814	1518	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	79.2001	604	1518	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.868	534	1518	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	78.0253	357	1518	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.6533	332	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:09,325] [INFO] DFAST Taxonomy check result was written to GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:20:09,326] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:09,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:09,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b64130c-59cf-4253-99aa-0ad34ffab983/dqc_reference/checkm_data
[2024-01-25 20:20:09,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:09,373] [INFO] Task started: CheckM
[2024-01-25 20:20:09,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/checkm_input GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:21:06,357] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:06,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:06,375] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:06,375] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:06,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:21:06,376] [INFO] Task started: Blastn
[2024-01-25 20:21:06,376] [INFO] Running command: blastn -query GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b64130c-59cf-4253-99aa-0ad34ffab983/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:07,235] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:07,238] [INFO] Selected 7 target genomes.
[2024-01-25 20:21:07,239] [INFO] Target genome list was writen to GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:07,243] [INFO] Task started: fastANI
[2024-01-25 20:21:07,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg8928e6a4-738a-43cd-a56a-9e29edce67cb/GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna.gz --refList GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:15,673] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:15,678] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:15,678] [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_900156345.1	s__Pontibacter indicus	100.0	1517	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014638845.1	s__Pontibacter amylolyticus	85.8243	1274	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846395.1	s__Pontibacter ramchanderi	84.7486	1178	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096355.1	s__Pontibacter virosus	84.2608	1179	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156415.1	s__Pontibacter lucknowensis	83.0569	1143	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	98.51	98.51	0.92	0.92	2	-
GCF_015686655.1	s__Pontibacter sp015686655	83.0179	1107	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773225.1	s__Pontibacter sp014773225	81.0109	813	1518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:15,680] [INFO] GTDB search result was written to GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:15,680] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:15,682] [INFO] DFAST_QC result json was written to GCF_900156345.1_IMG-taxon_2681812890_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:21:15,682] [INFO] DFAST_QC completed!
[2024-01-25 20:21:15,683] [INFO] Total running time: 0h1m40s