[2024-01-24 11:58:57,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,305] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8228f4f-5a44-4128-8da4-4d090ec44629/dqc_reference
[2024-01-24 11:58:58,631] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,632] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg68cd3557-4de6-4579-9e0c-eaa136177c36/GCF_011634895.1_ASM1163489v1_genomic.fna.gz | prodigal -d GCF_011634895.1_ASM1163489v1_genomic.fna/cds.fna -a GCF_011634895.1_ASM1163489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:08,496] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:08,497] [INFO] Task started: HMMsearch
[2024-01-24 11:59:08,497] [INFO] Running command: hmmsearch --tblout GCF_011634895.1_ASM1163489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8228f4f-5a44-4128-8da4-4d090ec44629/dqc_reference/reference_markers.hmm GCF_011634895.1_ASM1163489v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:08,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:08,832] [INFO] Found 6/6 markers.
[2024-01-24 11:59:08,863] [INFO] Query marker FASTA was written to GCF_011634895.1_ASM1163489v1_genomic.fna/markers.fasta
[2024-01-24 11:59:08,864] [INFO] Task started: Blastn
[2024-01-24 11:59:08,864] [INFO] Running command: blastn -query GCF_011634895.1_ASM1163489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8228f4f-5a44-4128-8da4-4d090ec44629/dqc_reference/reference_markers.fasta -out GCF_011634895.1_ASM1163489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:09,709] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:09,713] [INFO] Selected 9 target genomes.
[2024-01-24 11:59:09,714] [INFO] Target genome list was writen to GCF_011634895.1_ASM1163489v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:09,718] [INFO] Task started: fastANI
[2024-01-24 11:59:09,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg68cd3557-4de6-4579-9e0c-eaa136177c36/GCF_011634895.1_ASM1163489v1_genomic.fna.gz --refList GCF_011634895.1_ASM1163489v1_genomic.fna/target_genomes.txt --output GCF_011634895.1_ASM1163489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:18,002] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:18,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8228f4f-5a44-4128-8da4-4d090ec44629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:18,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8228f4f-5a44-4128-8da4-4d090ec44629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:18,012] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:18,012] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:18,013] [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 pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	100.0	1309	1310	95	conclusive
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	83.3193	888	1310	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	81.8875	780	1310	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	81.4042	769	1310	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	81.1647	767	1310	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	81.1395	757	1310	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	81.1006	769	1310	95	below_threshold
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	80.628	679	1310	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	80.0789	561	1310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:18,014] [INFO] DFAST Taxonomy check result was written to GCF_011634895.1_ASM1163489v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:18,015] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:18,015] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:18,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8228f4f-5a44-4128-8da4-4d090ec44629/dqc_reference/checkm_data
[2024-01-24 11:59:18,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:18,058] [INFO] Task started: CheckM
[2024-01-24 11:59:18,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011634895.1_ASM1163489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011634895.1_ASM1163489v1_genomic.fna/checkm_input GCF_011634895.1_ASM1163489v1_genomic.fna/checkm_result
[2024-01-24 11:59:51,956] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:51,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:51,980] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:51,980] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:51,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011634895.1_ASM1163489v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:51,980] [INFO] Task started: Blastn
[2024-01-24 11:59:51,980] [INFO] Running command: blastn -query GCF_011634895.1_ASM1163489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8228f4f-5a44-4128-8da4-4d090ec44629/dqc_reference/reference_markers_gtdb.fasta -out GCF_011634895.1_ASM1163489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:53,218] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:53,221] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:53,222] [INFO] Target genome list was writen to GCF_011634895.1_ASM1163489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:53,245] [INFO] Task started: fastANI
[2024-01-24 11:59:53,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg68cd3557-4de6-4579-9e0c-eaa136177c36/GCF_011634895.1_ASM1163489v1_genomic.fna.gz --refList GCF_011634895.1_ASM1163489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011634895.1_ASM1163489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:04,414] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:04,425] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:04,425] [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_011634895.1	s__Rheinheimera pleomorphica	100.0	1309	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000296695.1	s__Rheinheimera nanhaiensis	83.3193	888	1310	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	82.0966	809	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCF_013283795.1	s__Rheinheimera sp013283795	81.8779	781	1310	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	81.4043	769	1310	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	81.2647	783	1310	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	81.1492	775	1310	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	81.1003	752	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017824735.1	s__Rheinheimera sp017824735	81.0835	771	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004369005.1	s__Rheinheimera aquimaris	80.6836	708	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	-
GCF_000425345.1	s__Rheinheimera baltica	80.0816	561	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987765.1	s__Arsukibacterium sp000987765	78.0321	356	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:04,427] [INFO] GTDB search result was written to GCF_011634895.1_ASM1163489v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:04,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:04,431] [INFO] DFAST_QC result json was written to GCF_011634895.1_ASM1163489v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:04,431] [INFO] DFAST_QC completed!
[2024-01-24 12:00:04,431] [INFO] Total running time: 0h1m7s