[2024-01-24 14:22:04,139] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg8984c78f-bf9c-4561-a6b7-d278620c680c/dqc_reference
[2024-01-24 14:22:05,454] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,455] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg728a169a-5600-41fa-a5a2-bb85c1a26c9c/GCF_017824735.1_ASM1782473v1_genomic.fna.gz | prodigal -d GCF_017824735.1_ASM1782473v1_genomic.fna/cds.fna -a GCF_017824735.1_ASM1782473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:17,341] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:17,341] [INFO] Task started: HMMsearch
[2024-01-24 14:22:17,342] [INFO] Running command: hmmsearch --tblout GCF_017824735.1_ASM1782473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8984c78f-bf9c-4561-a6b7-d278620c680c/dqc_reference/reference_markers.hmm GCF_017824735.1_ASM1782473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:17,624] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:17,626] [INFO] Found 6/6 markers.
[2024-01-24 14:22:17,670] [INFO] Query marker FASTA was written to GCF_017824735.1_ASM1782473v1_genomic.fna/markers.fasta
[2024-01-24 14:22:17,670] [INFO] Task started: Blastn
[2024-01-24 14:22:17,670] [INFO] Running command: blastn -query GCF_017824735.1_ASM1782473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8984c78f-bf9c-4561-a6b7-d278620c680c/dqc_reference/reference_markers.fasta -out GCF_017824735.1_ASM1782473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:18,440] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:18,443] [INFO] Selected 9 target genomes.
[2024-01-24 14:22:18,444] [INFO] Target genome list was writen to GCF_017824735.1_ASM1782473v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:18,448] [INFO] Task started: fastANI
[2024-01-24 14:22:18,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg728a169a-5600-41fa-a5a2-bb85c1a26c9c/GCF_017824735.1_ASM1782473v1_genomic.fna.gz --refList GCF_017824735.1_ASM1782473v1_genomic.fna/target_genomes.txt --output GCF_017824735.1_ASM1782473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:26,491] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:26,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8984c78f-bf9c-4561-a6b7-d278620c680c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:26,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8984c78f-bf9c-4561-a6b7-d278620c680c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:26,501] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:26,501] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:26,501] [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 maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	100.0	1443	1444	95	conclusive
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	99.9978	1436	1444	95	conclusive
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	83.9678	765	1444	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	81.4008	712	1444	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	81.3766	726	1444	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	81.3427	628	1444	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	81.1785	768	1444	95	below_threshold
Alishewanella jeotgali	strain=KCTC 22429	GCA_000245735.2	545533	545533	type	True	78.314	290	1444	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	76.0758	60	1444	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:26,503] [INFO] DFAST Taxonomy check result was written to GCF_017824735.1_ASM1782473v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:26,503] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:26,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:26,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8984c78f-bf9c-4561-a6b7-d278620c680c/dqc_reference/checkm_data
[2024-01-24 14:22:26,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:26,547] [INFO] Task started: CheckM
[2024-01-24 14:22:26,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017824735.1_ASM1782473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017824735.1_ASM1782473v1_genomic.fna/checkm_input GCF_017824735.1_ASM1782473v1_genomic.fna/checkm_result
[2024-01-24 14:23:03,875] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:03,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.77%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:03,908] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:03,908] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:03,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017824735.1_ASM1782473v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:03,909] [INFO] Task started: Blastn
[2024-01-24 14:23:03,909] [INFO] Running command: blastn -query GCF_017824735.1_ASM1782473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8984c78f-bf9c-4561-a6b7-d278620c680c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017824735.1_ASM1782473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:04,816] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:04,819] [INFO] Selected 11 target genomes.
[2024-01-24 14:23:04,820] [INFO] Target genome list was writen to GCF_017824735.1_ASM1782473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:04,827] [INFO] Task started: fastANI
[2024-01-24 14:23:04,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg728a169a-5600-41fa-a5a2-bb85c1a26c9c/GCF_017824735.1_ASM1782473v1_genomic.fna.gz --refList GCF_017824735.1_ASM1782473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017824735.1_ASM1782473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:14,059] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:14,075] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:14,076] [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_017824735.1	s__Rheinheimera sp017824735	100.0	1443	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013283795.1	s__Rheinheimera sp013283795	83.959	766	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840125.1	s__Rheinheimera sp002840125	81.5664	728	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513785.1	s__Rheinheimera sp001513785	81.4631	724	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108485.1	s__Rheinheimera pacifica	81.3927	714	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425345.1	s__Rheinheimera baltica	81.3428	628	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011634895.1	s__Rheinheimera pleomorphica	81.1785	768	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	80.5381	683	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000245735.1	s__Alishewanella jeotgali	78.3121	289	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	N/A	N/A	N/A	N/A	1	-
GCF_000987765.1	s__Arsukibacterium sp000987765	78.061	338	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	76.0758	60	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:14,078] [INFO] GTDB search result was written to GCF_017824735.1_ASM1782473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:14,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:14,082] [INFO] DFAST_QC result json was written to GCF_017824735.1_ASM1782473v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:14,082] [INFO] DFAST_QC completed!
[2024-01-24 14:23:14,082] [INFO] Total running time: 0h1m10s