[2024-01-24 12:42:10,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:10,155] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:10,155] [INFO] DQC Reference Directory: /var/lib/cwl/stgb10efc30-805c-49fb-a2cc-91e3d0197888/dqc_reference
[2024-01-24 12:42:11,412] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:11,413] [INFO] Task started: Prodigal
[2024-01-24 12:42:11,413] [INFO] Running command: gunzip -c /var/lib/cwl/stgb68773c3-f0a4-49cc-91bb-01cdbf13a8fc/GCF_023630255.1_ASM2363025v1_genomic.fna.gz | prodigal -d GCF_023630255.1_ASM2363025v1_genomic.fna/cds.fna -a GCF_023630255.1_ASM2363025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:28,293] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:28,294] [INFO] Task started: HMMsearch
[2024-01-24 12:42:28,294] [INFO] Running command: hmmsearch --tblout GCF_023630255.1_ASM2363025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb10efc30-805c-49fb-a2cc-91e3d0197888/dqc_reference/reference_markers.hmm GCF_023630255.1_ASM2363025v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:28,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:28,612] [INFO] Found 6/6 markers.
[2024-01-24 12:42:28,653] [INFO] Query marker FASTA was written to GCF_023630255.1_ASM2363025v1_genomic.fna/markers.fasta
[2024-01-24 12:42:28,653] [INFO] Task started: Blastn
[2024-01-24 12:42:28,654] [INFO] Running command: blastn -query GCF_023630255.1_ASM2363025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb10efc30-805c-49fb-a2cc-91e3d0197888/dqc_reference/reference_markers.fasta -out GCF_023630255.1_ASM2363025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:29,264] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:29,267] [INFO] Selected 11 target genomes.
[2024-01-24 12:42:29,268] [INFO] Target genome list was writen to GCF_023630255.1_ASM2363025v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:29,271] [INFO] Task started: fastANI
[2024-01-24 12:42:29,271] [INFO] Running command: fastANI --query /var/lib/cwl/stgb68773c3-f0a4-49cc-91bb-01cdbf13a8fc/GCF_023630255.1_ASM2363025v1_genomic.fna.gz --refList GCF_023630255.1_ASM2363025v1_genomic.fna/target_genomes.txt --output GCF_023630255.1_ASM2363025v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:39,188] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:39,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb10efc30-805c-49fb-a2cc-91e3d0197888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:39,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb10efc30-805c-49fb-a2cc-91e3d0197888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:39,199] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:39,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:39,199] [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 deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	100.0	1380	1380	95	conclusive
Pontibacter fetidus	strain=BT213	GCA_010119545.1	2700082	2700082	type	True	82.625	875	1380	95	below_threshold
Pontibacter pudoricolor	strain=BT214	GCA_010092985.1	2694930	2694930	type	True	82.0079	866	1380	95	below_threshold
Pontibacter burrus	strain=BT327	GCA_010686685.1	2704466	2704466	type	True	80.9596	728	1380	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	79.1667	524	1380	95	below_threshold
Pontibacter lucknowensis	strain=DM9	GCA_900156415.1	1077936	1077936	type	True	78.2527	325	1380	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	78.2184	425	1380	95	below_threshold
Pontibacter indicus	strain=LP100	GCA_900156345.1	1317125	1317125	type	True	78.1327	351	1380	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.13	372	1380	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	77.9645	328	1380	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	77.7829	374	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:39,201] [INFO] DFAST Taxonomy check result was written to GCF_023630255.1_ASM2363025v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:39,202] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:39,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:39,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb10efc30-805c-49fb-a2cc-91e3d0197888/dqc_reference/checkm_data
[2024-01-24 12:42:39,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:39,248] [INFO] Task started: CheckM
[2024-01-24 12:42:39,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023630255.1_ASM2363025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023630255.1_ASM2363025v1_genomic.fna/checkm_input GCF_023630255.1_ASM2363025v1_genomic.fna/checkm_result
[2024-01-24 12:43:27,635] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:27,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:27,661] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:27,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:27,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023630255.1_ASM2363025v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:27,662] [INFO] Task started: Blastn
[2024-01-24 12:43:27,662] [INFO] Running command: blastn -query GCF_023630255.1_ASM2363025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb10efc30-805c-49fb-a2cc-91e3d0197888/dqc_reference/reference_markers_gtdb.fasta -out GCF_023630255.1_ASM2363025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:28,435] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:28,439] [INFO] Selected 7 target genomes.
[2024-01-24 12:43:28,439] [INFO] Target genome list was writen to GCF_023630255.1_ASM2363025v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:28,446] [INFO] Task started: fastANI
[2024-01-24 12:43:28,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgb68773c3-f0a4-49cc-91bb-01cdbf13a8fc/GCF_023630255.1_ASM2363025v1_genomic.fna.gz --refList GCF_023630255.1_ASM2363025v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023630255.1_ASM2363025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:35,615] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:35,629] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:35,630] [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_014297265.1	s__Pontibacter sp014297265	99.9987	1377	1380	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_010119545.1	s__Pontibacter fetidus	82.6489	872	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010092985.1	s__Pontibacter pudoricolor	82.0056	867	1380	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	82.0016	867	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014212495.1	s__Pontibacter sp014212495	81.2925	801	1380	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	80.942	731	1380	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	78.1098	352	1380	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 12:43:35,631] [INFO] GTDB search result was written to GCF_023630255.1_ASM2363025v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:35,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:35,636] [INFO] DFAST_QC result json was written to GCF_023630255.1_ASM2363025v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:35,636] [INFO] DFAST_QC completed!
[2024-01-24 12:43:35,636] [INFO] Total running time: 0h1m25s