[2024-01-24 11:58:54,400] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:54,402] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:54,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg859c7b0f-969b-48ec-b3b5-f9125b0f6ac9/dqc_reference
[2024-01-24 11:58:55,587] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:55,588] [INFO] Task started: Prodigal
[2024-01-24 11:58:55,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg979dc2ee-9388-437d-9ed7-88bba85e065b/GCF_014306105.1_ASM1430610v1_genomic.fna.gz | prodigal -d GCF_014306105.1_ASM1430610v1_genomic.fna/cds.fna -a GCF_014306105.1_ASM1430610v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:16,564] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:16,564] [INFO] Task started: HMMsearch
[2024-01-24 11:59:16,564] [INFO] Running command: hmmsearch --tblout GCF_014306105.1_ASM1430610v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg859c7b0f-969b-48ec-b3b5-f9125b0f6ac9/dqc_reference/reference_markers.hmm GCF_014306105.1_ASM1430610v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:16,962] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:16,964] [INFO] Found 6/6 markers.
[2024-01-24 11:59:17,016] [INFO] Query marker FASTA was written to GCF_014306105.1_ASM1430610v1_genomic.fna/markers.fasta
[2024-01-24 11:59:17,016] [INFO] Task started: Blastn
[2024-01-24 11:59:17,017] [INFO] Running command: blastn -query GCF_014306105.1_ASM1430610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg859c7b0f-969b-48ec-b3b5-f9125b0f6ac9/dqc_reference/reference_markers.fasta -out GCF_014306105.1_ASM1430610v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:17,628] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:17,631] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:17,632] [INFO] Target genome list was writen to GCF_014306105.1_ASM1430610v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:17,857] [INFO] Task started: fastANI
[2024-01-24 11:59:17,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg979dc2ee-9388-437d-9ed7-88bba85e065b/GCF_014306105.1_ASM1430610v1_genomic.fna.gz --refList GCF_014306105.1_ASM1430610v1_genomic.fna/target_genomes.txt --output GCF_014306105.1_ASM1430610v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:36,952] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:36,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg859c7b0f-969b-48ec-b3b5-f9125b0f6ac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:36,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg859c7b0f-969b-48ec-b3b5-f9125b0f6ac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:36,968] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:36,968] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:36,968] [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 cellulosilyticus	strain=SD6	GCA_014306105.1	1720253	1720253	type	True	100.0	1530	1532	95	conclusive
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	78.8691	462	1532	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.7104	486	1532	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.6332	482	1532	95	below_threshold
Pontibacter fetidus	strain=BT213	GCA_010119545.1	2700082	2700082	type	True	78.5118	461	1532	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	78.3896	464	1532	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	78.3626	457	1532	95	below_threshold
Pontibacter burrus	strain=BT327	GCA_010686685.1	2704466	2704466	type	True	78.2737	411	1532	95	below_threshold
Pontibacter korlensis	strain=X14-1T	GCA_000973725.1	400092	400092	type	True	78.2518	433	1532	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	78.2295	478	1532	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	78.221	478	1532	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	78.2173	479	1532	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	78.155	357	1532	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	78.128	373	1532	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	78.1142	458	1532	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_003002015.1	1610492	1610492	type	True	78.0932	371	1532	95	below_threshold
Pontibacter virosus	strain=DSM 100231	GCA_003096355.1	1765052	1765052	type	True	77.9345	352	1532	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	77.8415	327	1532	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.5989	250	1532	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:36,970] [INFO] DFAST Taxonomy check result was written to GCF_014306105.1_ASM1430610v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:36,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:36,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:36,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg859c7b0f-969b-48ec-b3b5-f9125b0f6ac9/dqc_reference/checkm_data
[2024-01-24 11:59:36,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:37,017] [INFO] Task started: CheckM
[2024-01-24 11:59:37,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014306105.1_ASM1430610v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014306105.1_ASM1430610v1_genomic.fna/checkm_input GCF_014306105.1_ASM1430610v1_genomic.fna/checkm_result
[2024-01-24 12:00:33,632] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:33,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:33,647] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:33,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:33,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014306105.1_ASM1430610v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:33,647] [INFO] Task started: Blastn
[2024-01-24 12:00:33,647] [INFO] Running command: blastn -query GCF_014306105.1_ASM1430610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg859c7b0f-969b-48ec-b3b5-f9125b0f6ac9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014306105.1_ASM1430610v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:34,409] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:34,412] [INFO] Selected 16 target genomes.
[2024-01-24 12:00:34,413] [INFO] Target genome list was writen to GCF_014306105.1_ASM1430610v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:34,422] [INFO] Task started: fastANI
[2024-01-24 12:00:34,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg979dc2ee-9388-437d-9ed7-88bba85e065b/GCF_014306105.1_ASM1430610v1_genomic.fna.gz --refList GCF_014306105.1_ASM1430610v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014306105.1_ASM1430610v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:49,046] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:49,059] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:49,059] [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_014306105.1	s__Pontibacter sp014306105	100.0	1530	1532	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_014297265.1	s__Pontibacter sp014297265	78.9797	443	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212495.1	s__Pontibacter sp014212495	78.9007	454	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122615.1	s__Pontibacter sp018122615	78.7654	431	1532	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	78.7235	485	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119545.1	s__Pontibacter fetidus	78.5252	460	1532	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	78.3682	466	1532	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	78.3598	458	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010686685.1	s__Pontibacter burrus	78.2548	413	1532	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	78.2518	433	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113285.1	s__Pontibacter chinhatensis	78.2463	475	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003585765.1	s__Pontibacter actiniarum	78.2126	478	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015686655.1	s__Pontibacter sp015686655	78.1731	360	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188175.1	s__Pontibacter ummariensis	78.148	371	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003576375.1	s__Pontibacter oryzae	78.1301	456	1532	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	77.9077	355	1532	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 12:00:49,061] [INFO] GTDB search result was written to GCF_014306105.1_ASM1430610v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:49,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:49,065] [INFO] DFAST_QC result json was written to GCF_014306105.1_ASM1430610v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:49,066] [INFO] DFAST_QC completed!
[2024-01-24 12:00:49,066] [INFO] Total running time: 0h1m55s