[2024-01-24 11:43:42,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,356] [INFO] DQC Reference Directory: /var/lib/cwl/stga7b8c15d-302e-4d95-800d-14f9a51583cf/dqc_reference
[2024-01-24 11:43:43,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,771] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,772] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2f8e075-c856-4767-8299-cd63b98b24c7/GCF_008017455.1_ASM801745v1_genomic.fna.gz | prodigal -d GCF_008017455.1_ASM801745v1_genomic.fna/cds.fna -a GCF_008017455.1_ASM801745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:11,041] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:11,041] [INFO] Task started: HMMsearch
[2024-01-24 11:44:11,041] [INFO] Running command: hmmsearch --tblout GCF_008017455.1_ASM801745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7b8c15d-302e-4d95-800d-14f9a51583cf/dqc_reference/reference_markers.hmm GCF_008017455.1_ASM801745v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:11,496] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:11,498] [INFO] Found 6/6 markers.
[2024-01-24 11:44:11,563] [INFO] Query marker FASTA was written to GCF_008017455.1_ASM801745v1_genomic.fna/markers.fasta
[2024-01-24 11:44:11,564] [INFO] Task started: Blastn
[2024-01-24 11:44:11,564] [INFO] Running command: blastn -query GCF_008017455.1_ASM801745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7b8c15d-302e-4d95-800d-14f9a51583cf/dqc_reference/reference_markers.fasta -out GCF_008017455.1_ASM801745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:12,220] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:12,224] [INFO] Selected 19 target genomes.
[2024-01-24 11:44:12,224] [INFO] Target genome list was writen to GCF_008017455.1_ASM801745v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:12,232] [INFO] Task started: fastANI
[2024-01-24 11:44:12,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2f8e075-c856-4767-8299-cd63b98b24c7/GCF_008017455.1_ASM801745v1_genomic.fna.gz --refList GCF_008017455.1_ASM801745v1_genomic.fna/target_genomes.txt --output GCF_008017455.1_ASM801745v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:28,580] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:28,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7b8c15d-302e-4d95-800d-14f9a51583cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:28,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7b8c15d-302e-4d95-800d-14f9a51583cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:28,599] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:28,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:28,600] [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 beigongshangensis	strain=T6-1	GCA_014332515.1	2574733	2574733	type	True	81.7709	1102	1967	95	below_threshold
Pontibacter virosus	strain=DSM 100231	GCA_003096355.1	1765052	1765052	type	True	78.628	351	1967	95	below_threshold
Botryobacter ruber	strain=SYSU D60016	GCA_003347595.2	2171629	2171629	type	True	78.2582	590	1967	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	78.0207	360	1967	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	78.0158	366	1967	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.9464	296	1967	95	below_threshold
Pontibacter roseus	strain=DSM 17521	GCA_000373265.1	336989	336989	type	True	77.8711	327	1967	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	77.7434	306	1967	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_003002015.1	1610492	1610492	type	True	77.7182	305	1967	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	77.6447	354	1967	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	77.6149	350	1967	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	77.6089	354	1967	95	below_threshold
Pontibacter burrus	strain=BT327	GCA_010686685.1	2704466	2704466	type	True	77.5654	268	1967	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	77.5653	306	1967	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	77.5551	279	1967	95	below_threshold
Pontibacter cellulosilyticus	strain=SD6	GCA_014306105.1	1720253	1720253	type	True	77.5149	265	1967	95	below_threshold
Pontibacter pudoricolor	strain=BT214	GCA_010092985.1	2694930	2694930	type	True	77.3652	283	1967	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.2929	240	1967	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:28,601] [INFO] DFAST Taxonomy check result was written to GCF_008017455.1_ASM801745v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:28,602] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:28,602] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:28,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7b8c15d-302e-4d95-800d-14f9a51583cf/dqc_reference/checkm_data
[2024-01-24 11:44:28,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:28,661] [INFO] Task started: CheckM
[2024-01-24 11:44:28,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008017455.1_ASM801745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008017455.1_ASM801745v1_genomic.fna/checkm_input GCF_008017455.1_ASM801745v1_genomic.fna/checkm_result
[2024-01-24 11:45:41,808] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:41,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:41,833] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:41,833] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:41,833] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008017455.1_ASM801745v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:41,834] [INFO] Task started: Blastn
[2024-01-24 11:45:41,834] [INFO] Running command: blastn -query GCF_008017455.1_ASM801745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7b8c15d-302e-4d95-800d-14f9a51583cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_008017455.1_ASM801745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:42,627] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:42,631] [INFO] Selected 11 target genomes.
[2024-01-24 11:45:42,632] [INFO] Target genome list was writen to GCF_008017455.1_ASM801745v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:42,642] [INFO] Task started: fastANI
[2024-01-24 11:45:42,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2f8e075-c856-4767-8299-cd63b98b24c7/GCF_008017455.1_ASM801745v1_genomic.fna.gz --refList GCF_008017455.1_ASM801745v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008017455.1_ASM801745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:53,739] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:53,754] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:53,754] [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_008017455.1	s__Botryobacter sp008017455	100.0	1959	1967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014332515.1	s__Botryobacter beigongshangensis	81.7638	1103	1967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005491705.1	s__SGAir0037 sp005491705	78.3581	344	1967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__SGAir0037	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347595.2	s__Botryobacter ruber	78.2644	589	1967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373265.1	s__Pontibacter roseus	77.8655	328	1967	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	77.7434	306	1967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010686685.1	s__Pontibacter burrus	77.5561	269	1967	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	77.5275	339	1967	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	77.5144	265	1967	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	77.3169	267	1967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015694705.1	s__Pontibacter sp015694705	77.2789	299	1967	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 11:45:53,756] [INFO] GTDB search result was written to GCF_008017455.1_ASM801745v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:53,756] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:53,760] [INFO] DFAST_QC result json was written to GCF_008017455.1_ASM801745v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:53,760] [INFO] DFAST_QC completed!
[2024-01-24 11:45:53,760] [INFO] Total running time: 0h2m11s