[2024-01-25 19:34:50,968] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:50,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:50,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg906a8db2-1489-4ad4-8053-919f793a6132/dqc_reference
[2024-01-25 19:34:52,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:52,091] [INFO] Task started: Prodigal
[2024-01-25 19:34:52,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f093e3b-381d-4027-87db-58c9fe7699a7/GCF_004005945.1_ASM400594v1_genomic.fna.gz | prodigal -d GCF_004005945.1_ASM400594v1_genomic.fna/cds.fna -a GCF_004005945.1_ASM400594v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:04,024] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:04,024] [INFO] Task started: HMMsearch
[2024-01-25 19:35:04,024] [INFO] Running command: hmmsearch --tblout GCF_004005945.1_ASM400594v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg906a8db2-1489-4ad4-8053-919f793a6132/dqc_reference/reference_markers.hmm GCF_004005945.1_ASM400594v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:04,286] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:04,287] [INFO] Found 6/6 markers.
[2024-01-25 19:35:04,323] [INFO] Query marker FASTA was written to GCF_004005945.1_ASM400594v1_genomic.fna/markers.fasta
[2024-01-25 19:35:04,323] [INFO] Task started: Blastn
[2024-01-25 19:35:04,324] [INFO] Running command: blastn -query GCF_004005945.1_ASM400594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg906a8db2-1489-4ad4-8053-919f793a6132/dqc_reference/reference_markers.fasta -out GCF_004005945.1_ASM400594v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:05,062] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:05,066] [INFO] Selected 13 target genomes.
[2024-01-25 19:35:05,066] [INFO] Target genome list was writen to GCF_004005945.1_ASM400594v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:05,070] [INFO] Task started: fastANI
[2024-01-25 19:35:05,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f093e3b-381d-4027-87db-58c9fe7699a7/GCF_004005945.1_ASM400594v1_genomic.fna.gz --refList GCF_004005945.1_ASM400594v1_genomic.fna/target_genomes.txt --output GCF_004005945.1_ASM400594v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:15,803] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:15,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg906a8db2-1489-4ad4-8053-919f793a6132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:15,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg906a8db2-1489-4ad4-8053-919f793a6132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:15,812] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:35:15,812] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:15,812] [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
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	100.0	1547	1552	95	conclusive
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	78.7307	531	1552	95	below_threshold
Rheinheimera tangshanensis	strain=JA3-B52	GCA_008017875.1	400153	400153	type	True	78.4824	326	1552	95	below_threshold
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	78.4134	329	1552	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	78.3845	339	1552	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	78.32	326	1552	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	77.7954	255	1552	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	77.6641	200	1552	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	77.6458	252	1552	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	77.6271	166	1552	95	below_threshold
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	77.5853	216	1552	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	77.5377	251	1552	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	77.4532	256	1552	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:15,815] [INFO] DFAST Taxonomy check result was written to GCF_004005945.1_ASM400594v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:15,816] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:15,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:15,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg906a8db2-1489-4ad4-8053-919f793a6132/dqc_reference/checkm_data
[2024-01-25 19:35:15,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:15,863] [INFO] Task started: CheckM
[2024-01-25 19:35:15,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005945.1_ASM400594v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005945.1_ASM400594v1_genomic.fna/checkm_input GCF_004005945.1_ASM400594v1_genomic.fna/checkm_result
[2024-01-25 19:35:54,584] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:54,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:54,609] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:54,609] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:54,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005945.1_ASM400594v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:54,611] [INFO] Task started: Blastn
[2024-01-25 19:35:54,611] [INFO] Running command: blastn -query GCF_004005945.1_ASM400594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg906a8db2-1489-4ad4-8053-919f793a6132/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005945.1_ASM400594v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:55,822] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:55,826] [INFO] Selected 8 target genomes.
[2024-01-25 19:35:55,827] [INFO] Target genome list was writen to GCF_004005945.1_ASM400594v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:55,834] [INFO] Task started: fastANI
[2024-01-25 19:35:55,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f093e3b-381d-4027-87db-58c9fe7699a7/GCF_004005945.1_ASM400594v1_genomic.fna.gz --refList GCF_004005945.1_ASM400594v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005945.1_ASM400594v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:04,332] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:04,338] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:04,338] [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_004005945.1	s__Pararheinheimera riviphila	100.0	1547	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001669775.1	s__Pararheinheimera sp001669775	89.4784	1322	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820995.1	s__Pararheinheimera sp018820995	81.9206	705	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.83	98.80	0.82	0.81	5	-
GCA_003543135.1	s__Pararheinheimera sp003543135	80.3867	668	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.83	98.83	0.95	0.95	2	-
GCF_000711985.1	s__Pararheinheimera texasensis	78.7309	530	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008015325.1	s__Pararheinheimera sp008015325	78.4898	461	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005375.1	s__Pararheinheimera sp004005375	78.2002	311	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018815765.1	s__Pararheinheimera sp018815765	77.6822	302	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:04,339] [INFO] GTDB search result was written to GCF_004005945.1_ASM400594v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:04,339] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:04,342] [INFO] DFAST_QC result json was written to GCF_004005945.1_ASM400594v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:04,342] [INFO] DFAST_QC completed!
[2024-01-25 19:36:04,342] [INFO] Total running time: 0h1m13s