[2024-01-25 19:45:50,444] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:50,445] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:50,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg68fa3f9b-9a99-4d1d-939e-0a1981822181/dqc_reference
[2024-01-25 19:45:51,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:51,704] [INFO] Task started: Prodigal
[2024-01-25 19:45:51,704] [INFO] Running command: gunzip -c /var/lib/cwl/stge40e029c-722f-45a0-b3ea-a24541f00e3c/GCF_003122215.1_ASM312221v1_genomic.fna.gz | prodigal -d GCF_003122215.1_ASM312221v1_genomic.fna/cds.fna -a GCF_003122215.1_ASM312221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:03,218] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:03,218] [INFO] Task started: HMMsearch
[2024-01-25 19:46:03,218] [INFO] Running command: hmmsearch --tblout GCF_003122215.1_ASM312221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68fa3f9b-9a99-4d1d-939e-0a1981822181/dqc_reference/reference_markers.hmm GCF_003122215.1_ASM312221v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:03,457] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:03,458] [INFO] Found 6/6 markers.
[2024-01-25 19:46:03,495] [INFO] Query marker FASTA was written to GCF_003122215.1_ASM312221v1_genomic.fna/markers.fasta
[2024-01-25 19:46:03,496] [INFO] Task started: Blastn
[2024-01-25 19:46:03,496] [INFO] Running command: blastn -query GCF_003122215.1_ASM312221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68fa3f9b-9a99-4d1d-939e-0a1981822181/dqc_reference/reference_markers.fasta -out GCF_003122215.1_ASM312221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:04,406] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:04,409] [INFO] Selected 20 target genomes.
[2024-01-25 19:46:04,409] [INFO] Target genome list was writen to GCF_003122215.1_ASM312221v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:04,424] [INFO] Task started: fastANI
[2024-01-25 19:46:04,425] [INFO] Running command: fastANI --query /var/lib/cwl/stge40e029c-722f-45a0-b3ea-a24541f00e3c/GCF_003122215.1_ASM312221v1_genomic.fna.gz --refList GCF_003122215.1_ASM312221v1_genomic.fna/target_genomes.txt --output GCF_003122215.1_ASM312221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:21,182] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:21,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68fa3f9b-9a99-4d1d-939e-0a1981822181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:21,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68fa3f9b-9a99-4d1d-939e-0a1981822181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:21,195] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:21,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:21,195] [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
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	100.0	1481	1482	95	conclusive
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	83.1475	1050	1482	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	83.0974	1055	1482	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	81.2344	924	1482	95	below_threshold
Pararhodobacter oceanensis	strain=AM505	GCA_003076755.1	2172121	2172121	type	True	78.806	606	1482	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.6268	487	1482	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.5155	502	1482	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	78.4571	502	1482	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.3499	490	1482	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.2437	419	1482	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.2217	463	1482	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.1447	453	1482	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.0628	446	1482	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.0495	459	1482	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	77.8748	422	1482	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.8182	391	1482	95	below_threshold
Caulobacter henricii	strain=CB4	GCA_001414055.1	69395	69395	type	True	76.1537	123	1482	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	76.0899	122	1482	95	below_threshold
Novosphingobium sediminicola	strain=DSM 27057	GCA_014196525.1	563162	563162	type	True	76.0045	137	1482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:21,197] [INFO] DFAST Taxonomy check result was written to GCF_003122215.1_ASM312221v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:21,197] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:21,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:21,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68fa3f9b-9a99-4d1d-939e-0a1981822181/dqc_reference/checkm_data
[2024-01-25 19:46:21,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:21,243] [INFO] Task started: CheckM
[2024-01-25 19:46:21,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003122215.1_ASM312221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003122215.1_ASM312221v1_genomic.fna/checkm_input GCF_003122215.1_ASM312221v1_genomic.fna/checkm_result
[2024-01-25 19:47:01,862] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:01,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:01,882] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:01,883] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:01,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003122215.1_ASM312221v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:01,883] [INFO] Task started: Blastn
[2024-01-25 19:47:01,883] [INFO] Running command: blastn -query GCF_003122215.1_ASM312221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68fa3f9b-9a99-4d1d-939e-0a1981822181/dqc_reference/reference_markers_gtdb.fasta -out GCF_003122215.1_ASM312221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:03,543] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:03,545] [INFO] Selected 11 target genomes.
[2024-01-25 19:47:03,546] [INFO] Target genome list was writen to GCF_003122215.1_ASM312221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:03,556] [INFO] Task started: fastANI
[2024-01-25 19:47:03,556] [INFO] Running command: fastANI --query /var/lib/cwl/stge40e029c-722f-45a0-b3ea-a24541f00e3c/GCF_003122215.1_ASM312221v1_genomic.fna.gz --refList GCF_003122215.1_ASM312221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003122215.1_ASM312221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:16,013] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:16,021] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:16,021] [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_003122215.1	s__Pararhodobacter marinus	100.0	1481	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017303295.1	s__Pararhodobacter sp017303295	90.0987	1260	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	83.1545	1048	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001691415.1	s__Pararhodobacter sp001691415	82.9043	1005	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990445.1	s__Pararhodobacter zhoushanensis	81.2106	928	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314715.1	s__Pararhodobacter sp001314715	78.948	584	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551925.1	s__PUOA01 sp003551925	78.4987	403	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300515.1	s__Nitratireductor indicus	76.1223	123	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002002725.1	s__Ensifer sp002002725	75.9866	150	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.52	98.52	0.94	0.94	2	-
GCF_002831585.1	s__Bradyrhizobium sp002831585	75.9852	197	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.70	98.62	0.95	0.93	5	-
GCA_016125405.1	s__UBA7672 sp016125405	75.8507	78	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:16,022] [INFO] GTDB search result was written to GCF_003122215.1_ASM312221v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:16,023] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:16,026] [INFO] DFAST_QC result json was written to GCF_003122215.1_ASM312221v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:16,026] [INFO] DFAST_QC completed!
[2024-01-25 19:47:16,026] [INFO] Total running time: 0h1m26s