[2024-01-25 17:46:35,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:35,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:35,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg203bd1fe-8f9a-489d-ad60-a39fae1d0d13/dqc_reference
[2024-01-25 17:46:36,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:36,737] [INFO] Task started: Prodigal
[2024-01-25 17:46:36,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f909733-14b2-42d2-a6b8-c74768c7376f/GCF_022436675.1_ASM2243667v1_genomic.fna.gz | prodigal -d GCF_022436675.1_ASM2243667v1_genomic.fna/cds.fna -a GCF_022436675.1_ASM2243667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:49,105] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:49,105] [INFO] Task started: HMMsearch
[2024-01-25 17:46:49,105] [INFO] Running command: hmmsearch --tblout GCF_022436675.1_ASM2243667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg203bd1fe-8f9a-489d-ad60-a39fae1d0d13/dqc_reference/reference_markers.hmm GCF_022436675.1_ASM2243667v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:49,438] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:49,439] [INFO] Found 6/6 markers.
[2024-01-25 17:46:49,474] [INFO] Query marker FASTA was written to GCF_022436675.1_ASM2243667v1_genomic.fna/markers.fasta
[2024-01-25 17:46:49,475] [INFO] Task started: Blastn
[2024-01-25 17:46:49,475] [INFO] Running command: blastn -query GCF_022436675.1_ASM2243667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg203bd1fe-8f9a-489d-ad60-a39fae1d0d13/dqc_reference/reference_markers.fasta -out GCF_022436675.1_ASM2243667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:50,301] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:50,304] [INFO] Selected 11 target genomes.
[2024-01-25 17:46:50,304] [INFO] Target genome list was writen to GCF_022436675.1_ASM2243667v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:50,316] [INFO] Task started: fastANI
[2024-01-25 17:46:50,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f909733-14b2-42d2-a6b8-c74768c7376f/GCF_022436675.1_ASM2243667v1_genomic.fna.gz --refList GCF_022436675.1_ASM2243667v1_genomic.fna/target_genomes.txt --output GCF_022436675.1_ASM2243667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:00,110] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:00,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg203bd1fe-8f9a-489d-ad60-a39fae1d0d13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:00,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg203bd1fe-8f9a-489d-ad60-a39fae1d0d13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:00,119] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:47:00,119] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:00,119] [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 hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	100.0	1547	1549	95	conclusive
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	90.472	1195	1549	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	82.811	908	1549	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	81.2113	731	1549	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	81.211	719	1549	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	81.1724	737	1549	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	80.9215	739	1549	95	below_threshold
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	80.6297	709	1549	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	76.1571	52	1549	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	75.8903	60	1549	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	75.8598	61	1549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:00,120] [INFO] DFAST Taxonomy check result was written to GCF_022436675.1_ASM2243667v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:00,121] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:00,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:00,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg203bd1fe-8f9a-489d-ad60-a39fae1d0d13/dqc_reference/checkm_data
[2024-01-25 17:47:00,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:00,166] [INFO] Task started: CheckM
[2024-01-25 17:47:00,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022436675.1_ASM2243667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022436675.1_ASM2243667v1_genomic.fna/checkm_input GCF_022436675.1_ASM2243667v1_genomic.fna/checkm_result
[2024-01-25 17:47:38,437] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:38,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:38,455] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:38,455] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:38,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022436675.1_ASM2243667v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:38,456] [INFO] Task started: Blastn
[2024-01-25 17:47:38,456] [INFO] Running command: blastn -query GCF_022436675.1_ASM2243667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg203bd1fe-8f9a-489d-ad60-a39fae1d0d13/dqc_reference/reference_markers_gtdb.fasta -out GCF_022436675.1_ASM2243667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:39,642] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:39,644] [INFO] Selected 9 target genomes.
[2024-01-25 17:47:39,645] [INFO] Target genome list was writen to GCF_022436675.1_ASM2243667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:39,666] [INFO] Task started: fastANI
[2024-01-25 17:47:39,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f909733-14b2-42d2-a6b8-c74768c7376f/GCF_022436675.1_ASM2243667v1_genomic.fna.gz --refList GCF_022436675.1_ASM2243667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022436675.1_ASM2243667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:49,122] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:49,129] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:47:49,129] [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_001513785.1	s__Rheinheimera sp001513785	94.1141	1286	1549	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	90.4586	1196	1549	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	89.9074	1249	1549	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	88.1517	1183	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013283795.1	s__Rheinheimera sp013283795	82.8111	908	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017824735.1	s__Rheinheimera sp017824735	81.2198	718	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011634895.1	s__Rheinheimera pleomorphica	81.1777	736	1549	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	80.7797	764	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCA_018825965.1	s__Pararheinheimera sp018825965	77.4819	269	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	99.98	99.95	0.98	0.97	7	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:49,131] [INFO] GTDB search result was written to GCF_022436675.1_ASM2243667v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:49,131] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:49,134] [INFO] DFAST_QC result json was written to GCF_022436675.1_ASM2243667v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:49,134] [INFO] DFAST_QC completed!
[2024-01-25 17:47:49,134] [INFO] Total running time: 0h1m14s