[2024-01-25 20:00:05,900] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:05,901] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:05,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg15fdfcfe-cfd9-4e58-a6e0-ef2c1d10ebf9/dqc_reference
[2024-01-25 20:00:07,141] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:07,142] [INFO] Task started: Prodigal
[2024-01-25 20:00:07,142] [INFO] Running command: gunzip -c /var/lib/cwl/stg65e606b5-a7cb-4daf-a053-620356a98eb2/GCF_003002015.1_ASM300201v1_genomic.fna.gz | prodigal -d GCF_003002015.1_ASM300201v1_genomic.fna/cds.fna -a GCF_003002015.1_ASM300201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:31,315] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:31,315] [INFO] Task started: HMMsearch
[2024-01-25 20:00:31,315] [INFO] Running command: hmmsearch --tblout GCF_003002015.1_ASM300201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15fdfcfe-cfd9-4e58-a6e0-ef2c1d10ebf9/dqc_reference/reference_markers.hmm GCF_003002015.1_ASM300201v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:31,568] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:31,569] [INFO] Found 6/6 markers.
[2024-01-25 20:00:31,614] [INFO] Query marker FASTA was written to GCF_003002015.1_ASM300201v1_genomic.fna/markers.fasta
[2024-01-25 20:00:31,614] [INFO] Task started: Blastn
[2024-01-25 20:00:31,614] [INFO] Running command: blastn -query GCF_003002015.1_ASM300201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15fdfcfe-cfd9-4e58-a6e0-ef2c1d10ebf9/dqc_reference/reference_markers.fasta -out GCF_003002015.1_ASM300201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:32,179] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:32,181] [INFO] Selected 13 target genomes.
[2024-01-25 20:00:32,181] [INFO] Target genome list was writen to GCF_003002015.1_ASM300201v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:32,200] [INFO] Task started: fastANI
[2024-01-25 20:00:32,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e606b5-a7cb-4daf-a053-620356a98eb2/GCF_003002015.1_ASM300201v1_genomic.fna.gz --refList GCF_003002015.1_ASM300201v1_genomic.fna/target_genomes.txt --output GCF_003002015.1_ASM300201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:44,582] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:44,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15fdfcfe-cfd9-4e58-a6e0-ef2c1d10ebf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:44,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15fdfcfe-cfd9-4e58-a6e0-ef2c1d10ebf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:44,591] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:00:44,591] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:44,591] [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 ummariensis	strain=NKM1	GCA_003002015.1	1610492	1610492	type	True	100.0	1943	1946	95	conclusive
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	99.9987	1943	1946	95	conclusive
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	79.3475	637	1946	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	79.2747	637	1946	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.8451	574	1946	95	below_threshold
Pontibacter korlensis	strain=X14-1T	GCA_000973725.1	400092	400092	type	True	78.6711	449	1946	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	78.6695	545	1946	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	78.4313	536	1946	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	78.4013	511	1946	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.1573	429	1946	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	77.8502	331	1946	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	77.5893	301	1946	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.5685	277	1946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:44,593] [INFO] DFAST Taxonomy check result was written to GCF_003002015.1_ASM300201v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:44,594] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:44,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:44,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15fdfcfe-cfd9-4e58-a6e0-ef2c1d10ebf9/dqc_reference/checkm_data
[2024-01-25 20:00:44,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:44,652] [INFO] Task started: CheckM
[2024-01-25 20:00:44,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002015.1_ASM300201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002015.1_ASM300201v1_genomic.fna/checkm_input GCF_003002015.1_ASM300201v1_genomic.fna/checkm_result
[2024-01-25 20:01:47,375] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:47,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:47,398] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:47,398] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:47,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002015.1_ASM300201v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:47,399] [INFO] Task started: Blastn
[2024-01-25 20:01:47,399] [INFO] Running command: blastn -query GCF_003002015.1_ASM300201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15fdfcfe-cfd9-4e58-a6e0-ef2c1d10ebf9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002015.1_ASM300201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:48,184] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:48,190] [INFO] Selected 12 target genomes.
[2024-01-25 20:01:48,190] [INFO] Target genome list was writen to GCF_003002015.1_ASM300201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:48,203] [INFO] Task started: fastANI
[2024-01-25 20:01:48,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e606b5-a7cb-4daf-a053-620356a98eb2/GCF_003002015.1_ASM300201v1_genomic.fna.gz --refList GCF_003002015.1_ASM300201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002015.1_ASM300201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:59,925] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:59,933] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:59,933] [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_900188175.1	s__Pontibacter ummariensis	99.9987	1943	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003585765.1	s__Pontibacter actiniarum	79.3439	638	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006385705.1	s__Pontibacter sp006385705	78.8675	571	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054055.1	s__Pontibacter mucosus	78.6907	542	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973725.1	s__Pontibacter korlensis	78.6528	451	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907195.1	s__Pontibacter sp001907195	78.4241	537	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611675.1	s__Pontibacter akesuensis	78.4074	503	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900113285.1	s__Pontibacter chinhatensis	78.4037	512	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576375.1	s__Pontibacter oryzae	78.3874	430	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367245.1	s__Pontibacter diazotrophicus	78.3441	607	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931655.1	s__Pontibacter russatus	78.1197	517	1946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014306105.1	s__Pontibacter sp014306105	78.0255	392	1946	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 20:01:59,935] [INFO] GTDB search result was written to GCF_003002015.1_ASM300201v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:59,935] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:59,938] [INFO] DFAST_QC result json was written to GCF_003002015.1_ASM300201v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:59,938] [INFO] DFAST_QC completed!
[2024-01-25 20:01:59,938] [INFO] Total running time: 0h1m54s