[2024-01-24 13:09:51,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,816] [INFO] DQC Reference Directory: /var/lib/cwl/stge4f563fb-1a86-4c70-b4ca-abfad3f6d645/dqc_reference
[2024-01-24 13:09:53,225] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:53,226] [INFO] Task started: Prodigal
[2024-01-24 13:09:53,226] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e3e4ed3-9111-47fe-8cb0-e16d108ed1d1/GCF_020531985.1_ASM2053198v1_genomic.fna.gz | prodigal -d GCF_020531985.1_ASM2053198v1_genomic.fna/cds.fna -a GCF_020531985.1_ASM2053198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:04,515] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:04,515] [INFO] Task started: HMMsearch
[2024-01-24 13:10:04,515] [INFO] Running command: hmmsearch --tblout GCF_020531985.1_ASM2053198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4f563fb-1a86-4c70-b4ca-abfad3f6d645/dqc_reference/reference_markers.hmm GCF_020531985.1_ASM2053198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:04,881] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:04,882] [INFO] Found 6/6 markers.
[2024-01-24 13:10:04,927] [INFO] Query marker FASTA was written to GCF_020531985.1_ASM2053198v1_genomic.fna/markers.fasta
[2024-01-24 13:10:04,927] [INFO] Task started: Blastn
[2024-01-24 13:10:04,928] [INFO] Running command: blastn -query GCF_020531985.1_ASM2053198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4f563fb-1a86-4c70-b4ca-abfad3f6d645/dqc_reference/reference_markers.fasta -out GCF_020531985.1_ASM2053198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:05,724] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:05,727] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:05,727] [INFO] Target genome list was writen to GCF_020531985.1_ASM2053198v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:05,731] [INFO] Task started: fastANI
[2024-01-24 13:10:05,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3e4ed3-9111-47fe-8cb0-e16d108ed1d1/GCF_020531985.1_ASM2053198v1_genomic.fna.gz --refList GCF_020531985.1_ASM2053198v1_genomic.fna/target_genomes.txt --output GCF_020531985.1_ASM2053198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:16,340] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:16,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4f563fb-1a86-4c70-b4ca-abfad3f6d645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:16,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4f563fb-1a86-4c70-b4ca-abfad3f6d645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:16,350] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:16,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:16,351] [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 aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	100.0	1401	1402	95	conclusive
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	80.8256	661	1402	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	80.5983	672	1402	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	80.5027	722	1402	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	80.4313	697	1402	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	80.3566	751	1402	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	80.0323	604	1402	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	79.7339	525	1402	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	78.4761	242	1402	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	76.5261	52	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:16,352] [INFO] DFAST Taxonomy check result was written to GCF_020531985.1_ASM2053198v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:16,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:16,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:16,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4f563fb-1a86-4c70-b4ca-abfad3f6d645/dqc_reference/checkm_data
[2024-01-24 13:10:16,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:16,398] [INFO] Task started: CheckM
[2024-01-24 13:10:16,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020531985.1_ASM2053198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020531985.1_ASM2053198v1_genomic.fna/checkm_input GCF_020531985.1_ASM2053198v1_genomic.fna/checkm_result
[2024-01-24 13:10:52,433] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:52,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:52,456] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:52,457] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:52,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020531985.1_ASM2053198v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:52,457] [INFO] Task started: Blastn
[2024-01-24 13:10:52,458] [INFO] Running command: blastn -query GCF_020531985.1_ASM2053198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4f563fb-1a86-4c70-b4ca-abfad3f6d645/dqc_reference/reference_markers_gtdb.fasta -out GCF_020531985.1_ASM2053198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:53,663] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:53,668] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:53,668] [INFO] Target genome list was writen to GCF_020531985.1_ASM2053198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:53,679] [INFO] Task started: fastANI
[2024-01-24 13:10:53,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3e4ed3-9111-47fe-8cb0-e16d108ed1d1/GCF_020531985.1_ASM2053198v1_genomic.fna.gz --refList GCF_020531985.1_ASM2053198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020531985.1_ASM2053198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:04,530] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:04,541] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:04,541] [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_004369005.1	s__Rheinheimera aquimaris	97.4497	1285	1402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	conclusive
GCF_000296695.1	s__Rheinheimera nanhaiensis	80.8316	660	1402	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	80.5867	674	1402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018831085.1	s__Rheinheimera sp018831085	80.5471	714	1402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002840125.1	s__Rheinheimera sp002840125	80.5401	748	1402	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	80.4601	769	1402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283795.1	s__Rheinheimera sp013283795	80.44	696	1402	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	80.3579	750	1402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826295.1	s__Rheinheimera sp018826295	80.1307	674	1402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCF_000425345.1	s__Rheinheimera baltica	79.744	524	1402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001752395.1	s__Rheinheimera salexigens	78.4912	240	1402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005375.1	s__Pararheinheimera sp004005375	77.7809	211	1402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:04,543] [INFO] GTDB search result was written to GCF_020531985.1_ASM2053198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:04,543] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:04,548] [INFO] DFAST_QC result json was written to GCF_020531985.1_ASM2053198v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:04,548] [INFO] DFAST_QC completed!
[2024-01-24 13:11:04,549] [INFO] Total running time: 0h1m13s