[2024-01-25 19:47:35,540] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:35,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:35,542] [INFO] DQC Reference Directory: /var/lib/cwl/stge8643c9a-075c-4f5d-8d74-bdc39cab3bfb/dqc_reference
[2024-01-25 19:47:36,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:36,716] [INFO] Task started: Prodigal
[2024-01-25 19:47:36,716] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e3f172b-e8c2-4bd6-814a-b5ff79d6b90e/GCF_016623615.1_ASM1662361v1_genomic.fna.gz | prodigal -d GCF_016623615.1_ASM1662361v1_genomic.fna/cds.fna -a GCF_016623615.1_ASM1662361v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:52,743] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:52,743] [INFO] Task started: HMMsearch
[2024-01-25 19:47:52,743] [INFO] Running command: hmmsearch --tblout GCF_016623615.1_ASM1662361v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8643c9a-075c-4f5d-8d74-bdc39cab3bfb/dqc_reference/reference_markers.hmm GCF_016623615.1_ASM1662361v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:53,008] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:53,009] [INFO] Found 6/6 markers.
[2024-01-25 19:47:53,045] [INFO] Query marker FASTA was written to GCF_016623615.1_ASM1662361v1_genomic.fna/markers.fasta
[2024-01-25 19:47:53,045] [INFO] Task started: Blastn
[2024-01-25 19:47:53,045] [INFO] Running command: blastn -query GCF_016623615.1_ASM1662361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8643c9a-075c-4f5d-8d74-bdc39cab3bfb/dqc_reference/reference_markers.fasta -out GCF_016623615.1_ASM1662361v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:53,609] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:53,611] [INFO] Selected 19 target genomes.
[2024-01-25 19:47:53,611] [INFO] Target genome list was writen to GCF_016623615.1_ASM1662361v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:53,622] [INFO] Task started: fastANI
[2024-01-25 19:47:53,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e3f172b-e8c2-4bd6-814a-b5ff79d6b90e/GCF_016623615.1_ASM1662361v1_genomic.fna.gz --refList GCF_016623615.1_ASM1662361v1_genomic.fna/target_genomes.txt --output GCF_016623615.1_ASM1662361v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:09,483] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:09,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8643c9a-075c-4f5d-8d74-bdc39cab3bfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:09,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8643c9a-075c-4f5d-8d74-bdc39cab3bfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:09,493] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:48:09,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:09,493] [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
Adhaeribacter terrigena	strain=BT258	GCA_016623615.1	2793070	2793070	type	True	100.0	1467	1468	95	conclusive
Adhaeribacter soli	strain=MA2	GCA_008727925.1	2607655	2607655	type	True	81.2038	795	1468	95	below_threshold
Pontibacter amylolyticus	strain=CGMCC 1.12749	GCA_014638845.1	1424080	1424080	type	True	76.6777	135	1468	95	below_threshold
Pontibacter cellulosilyticus	strain=SD6	GCA_014306105.1	1720253	1720253	type	True	76.6555	97	1468	95	below_threshold
Adhaeribacter aerolatus	strain=NBRC 106133	GCA_007991635.1	670289	670289	type	True	76.6245	195	1468	95	below_threshold
Pontibacter burrus	strain=BT327	GCA_010686685.1	2704466	2704466	type	True	76.4961	155	1468	95	below_threshold
Pontibacter fetidus	strain=BT213	GCA_010119545.1	2700082	2700082	type	True	76.4429	168	1468	95	below_threshold
Rufibacter radiotolerans	strain=DG31D	GCA_001078055.1	1379910	1379910	type	True	76.425	128	1468	95	below_threshold
Pontibacter beigongshangensis	strain=T6-1	GCA_014332515.1	2574733	2574733	type	True	76.3832	150	1468	95	below_threshold
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	76.3003	151	1468	95	below_threshold
Adhaeribacter swui	strain=KCTC 52873	GCA_014217805.1	2086471	2086471	type	True	76.2968	156	1468	95	below_threshold
Botryobacter ruber	strain=SYSU D60016	GCA_003347595.2	2171629	2171629	type	True	76.2668	174	1468	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	76.2542	165	1468	95	below_threshold
Rufibacter glacialis	strain=MDT1-10-3	GCA_008271745.1	1259555	1259555	type	True	76.2112	122	1468	95	below_threshold
Pontibacter roseus	strain=DSM 17521	GCA_000373265.1	336989	336989	type	True	75.8545	100	1468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:09,495] [INFO] DFAST Taxonomy check result was written to GCF_016623615.1_ASM1662361v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:09,495] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:09,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:09,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8643c9a-075c-4f5d-8d74-bdc39cab3bfb/dqc_reference/checkm_data
[2024-01-25 19:48:09,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:09,540] [INFO] Task started: CheckM
[2024-01-25 19:48:09,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016623615.1_ASM1662361v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016623615.1_ASM1662361v1_genomic.fna/checkm_input GCF_016623615.1_ASM1662361v1_genomic.fna/checkm_result
[2024-01-25 19:48:53,906] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:53,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:53,925] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:53,925] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:53,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016623615.1_ASM1662361v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:53,926] [INFO] Task started: Blastn
[2024-01-25 19:48:53,926] [INFO] Running command: blastn -query GCF_016623615.1_ASM1662361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8643c9a-075c-4f5d-8d74-bdc39cab3bfb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016623615.1_ASM1662361v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:54,778] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:54,781] [INFO] Selected 19 target genomes.
[2024-01-25 19:48:54,781] [INFO] Target genome list was writen to GCF_016623615.1_ASM1662361v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:54,806] [INFO] Task started: fastANI
[2024-01-25 19:48:54,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e3f172b-e8c2-4bd6-814a-b5ff79d6b90e/GCF_016623615.1_ASM1662361v1_genomic.fna.gz --refList GCF_016623615.1_ASM1662361v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016623615.1_ASM1662361v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:11,431] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:11,444] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:11,444] [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_016623615.1	s__Adhaeribacter_A sp016623615	100.0	1467	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008727925.1	s__Adhaeribacter_A soli	81.2371	790	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014269285.1	s__Rufibacter sediminis	76.7029	138	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212495.1	s__Pontibacter sp014212495	76.7013	191	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638845.1	s__Pontibacter amylolyticus	76.6777	135	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629685.1	s__Adhaeribacter rhizoryzae	76.6774	210	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014306105.1	s__Pontibacter sp014306105	76.6555	97	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991635.1	s__Adhaeribacter aerolatus	76.6245	195	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010686685.1	s__Pontibacter burrus	76.4961	155	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078055.1	s__Rufibacter radiotolerans	76.4108	129	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122615.1	s__Pontibacter sp018122615	76.3704	165	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014332515.1	s__Botryobacter beigongshangensis	76.3568	152	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001577755.1	s__Nibribacter sp001577755	76.3441	77	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Nibribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907195.1	s__Pontibacter sp001907195	76.2746	144	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347595.2	s__Botryobacter ruber	76.2668	174	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271745.1	s__Rufibacter glacialis	76.2112	122	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015694705.1	s__Pontibacter sp015694705	76.1917	132	1468	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	75.8545	100	1468	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 19:49:11,445] [INFO] GTDB search result was written to GCF_016623615.1_ASM1662361v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:11,446] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:11,449] [INFO] DFAST_QC result json was written to GCF_016623615.1_ASM1662361v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:11,449] [INFO] DFAST_QC completed!
[2024-01-25 19:49:11,449] [INFO] Total running time: 0h1m36s