[2024-01-24 10:47:40,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c6677dd-8002-4442-86b2-8550c63e5ef6/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgffe65812-ff49-458f-a489-5c22f987e286/GCF_014773225.1_ASM1477322v1_genomic.fna.gz | prodigal -d GCF_014773225.1_ASM1477322v1_genomic.fna/cds.fna -a GCF_014773225.1_ASM1477322v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:07,206] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:07,207] [INFO] Task started: HMMsearch
[2024-01-24 10:48:07,207] [INFO] Running command: hmmsearch --tblout GCF_014773225.1_ASM1477322v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c6677dd-8002-4442-86b2-8550c63e5ef6/dqc_reference/reference_markers.hmm GCF_014773225.1_ASM1477322v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:07,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:07,479] [INFO] Found 6/6 markers.
[2024-01-24 10:48:07,515] [INFO] Query marker FASTA was written to GCF_014773225.1_ASM1477322v1_genomic.fna/markers.fasta
[2024-01-24 10:48:07,516] [INFO] Task started: Blastn
[2024-01-24 10:48:07,516] [INFO] Running command: blastn -query GCF_014773225.1_ASM1477322v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c6677dd-8002-4442-86b2-8550c63e5ef6/dqc_reference/reference_markers.fasta -out GCF_014773225.1_ASM1477322v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:08,126] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:08,132] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:08,132] [INFO] Target genome list was writen to GCF_014773225.1_ASM1477322v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:08,177] [INFO] Task started: fastANI
[2024-01-24 10:48:08,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgffe65812-ff49-458f-a489-5c22f987e286/GCF_014773225.1_ASM1477322v1_genomic.fna.gz --refList GCF_014773225.1_ASM1477322v1_genomic.fna/target_genomes.txt --output GCF_014773225.1_ASM1477322v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:19,209] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:19,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c6677dd-8002-4442-86b2-8550c63e5ef6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:19,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c6677dd-8002-4442-86b2-8550c63e5ef6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:19,220] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:19,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:19,220] [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 aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	100.0	1360	1362	95	conclusive
Pontibacter amylolyticus	strain=CGMCC 1.12749	GCA_014638845.1	1424080	1424080	type	True	81.308	833	1362	95	below_threshold
Pontibacter lucknowensis	strain=DM9	GCA_900156415.1	1077936	1077936	type	True	81.2753	830	1362	95	below_threshold
Pontibacter virosus	strain=DSM 100231	GCA_003096355.1	1765052	1765052	type	True	81.2376	825	1362	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	81.1835	819	1362	95	below_threshold
Pontibacter indicus	strain=LP100	GCA_900156345.1	1317125	1317125	type	True	81.0317	832	1362	95	below_threshold
Pontibacter roseus	strain=DSM 17521	GCA_000373265.1	336989	336989	type	True	80.1729	742	1362	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.7319	523	1362	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	78.1348	310	1362	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	77.5914	336	1362	95	below_threshold
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	76.4804	147	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:19,222] [INFO] DFAST Taxonomy check result was written to GCF_014773225.1_ASM1477322v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:19,223] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:19,223] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:19,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c6677dd-8002-4442-86b2-8550c63e5ef6/dqc_reference/checkm_data
[2024-01-24 10:48:19,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:19,264] [INFO] Task started: CheckM
[2024-01-24 10:48:19,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014773225.1_ASM1477322v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014773225.1_ASM1477322v1_genomic.fna/checkm_input GCF_014773225.1_ASM1477322v1_genomic.fna/checkm_result
[2024-01-24 10:49:20,899] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:20,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:20,919] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:20,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:20,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014773225.1_ASM1477322v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:20,920] [INFO] Task started: Blastn
[2024-01-24 10:49:20,920] [INFO] Running command: blastn -query GCF_014773225.1_ASM1477322v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c6677dd-8002-4442-86b2-8550c63e5ef6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014773225.1_ASM1477322v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:21,748] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:21,755] [INFO] Selected 8 target genomes.
[2024-01-24 10:49:21,755] [INFO] Target genome list was writen to GCF_014773225.1_ASM1477322v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:21,762] [INFO] Task started: fastANI
[2024-01-24 10:49:21,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgffe65812-ff49-458f-a489-5c22f987e286/GCF_014773225.1_ASM1477322v1_genomic.fna.gz --refList GCF_014773225.1_ASM1477322v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014773225.1_ASM1477322v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:30,319] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:30,331] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:30,332] [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_014773225.1	s__Pontibacter sp014773225	100.0	1360	1362	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	81.308	833	1362	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	81.2751	829	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	98.51	98.51	0.92	0.92	2	-
GCF_003096355.1	s__Pontibacter virosus	81.2519	822	1362	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	81.1721	821	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686655.1	s__Pontibacter sp015686655	81.1607	823	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156345.1	s__Pontibacter indicus	81.0115	834	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373265.1	s__Pontibacter roseus	80.1729	742	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:30,335] [INFO] GTDB search result was written to GCF_014773225.1_ASM1477322v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:30,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:30,338] [INFO] DFAST_QC result json was written to GCF_014773225.1_ASM1477322v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:30,338] [INFO] DFAST_QC completed!
[2024-01-24 10:49:30,338] [INFO] Total running time: 0h1m49s