[2024-01-24 14:38:45,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,557] [INFO] DQC Reference Directory: /var/lib/cwl/stga2475a25-97c4-40cb-854d-37839f437dcc/dqc_reference
[2024-01-24 14:38:48,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,276] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,277] [INFO] Running command: gunzip -c /var/lib/cwl/stgb17a80b7-a42a-4c43-bd6f-1575501245a5/GCF_003987175.1_ASM398717v1_genomic.fna.gz | prodigal -d GCF_003987175.1_ASM398717v1_genomic.fna/cds.fna -a GCF_003987175.1_ASM398717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:55,994] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:55,995] [INFO] Task started: HMMsearch
[2024-01-24 14:38:55,995] [INFO] Running command: hmmsearch --tblout GCF_003987175.1_ASM398717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2475a25-97c4-40cb-854d-37839f437dcc/dqc_reference/reference_markers.hmm GCF_003987175.1_ASM398717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:56,223] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:56,225] [INFO] Found 6/6 markers.
[2024-01-24 14:38:56,252] [INFO] Query marker FASTA was written to GCF_003987175.1_ASM398717v1_genomic.fna/markers.fasta
[2024-01-24 14:38:56,252] [INFO] Task started: Blastn
[2024-01-24 14:38:56,253] [INFO] Running command: blastn -query GCF_003987175.1_ASM398717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2475a25-97c4-40cb-854d-37839f437dcc/dqc_reference/reference_markers.fasta -out GCF_003987175.1_ASM398717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:57,018] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:57,022] [INFO] Selected 25 target genomes.
[2024-01-24 14:38:57,023] [INFO] Target genome list was writen to GCF_003987175.1_ASM398717v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:57,132] [INFO] Task started: fastANI
[2024-01-24 14:38:57,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgb17a80b7-a42a-4c43-bd6f-1575501245a5/GCF_003987175.1_ASM398717v1_genomic.fna.gz --refList GCF_003987175.1_ASM398717v1_genomic.fna/target_genomes.txt --output GCF_003987175.1_ASM398717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:11,892] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:11,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2475a25-97c4-40cb-854d-37839f437dcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:11,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2475a25-97c4-40cb-854d-37839f437dcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:11,905] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:11,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:11,905] [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
Aliidiomarina sanyensis	strain=GYP-17	GCA_003987175.1	1249555	1249555	type	True	100.0	842	845	95	conclusive
Aliidiomarina haloalkalitolerans	strain=AK5	GCA_003987315.1	859059	859059	type	True	79.181	143	845	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	79.0612	225	845	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	78.7782	226	845	95	below_threshold
Aliidiomarina shirensis	strain=AIS	GCA_003987345.1	1048642	1048642	type	True	78.5276	125	845	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	78.3938	62	845	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	78.119	57	845	95	below_threshold
Aliidiomarina sedimenti	strain=GBSy1	GCA_003986955.1	1933879	1933879	type	True	78.0385	67	845	95	below_threshold
Pseudidiomarina insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	77.8919	50	845	95	below_threshold
Pseudidiomarina atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	77.5877	52	845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:11,913] [INFO] DFAST Taxonomy check result was written to GCF_003987175.1_ASM398717v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:11,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:11,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:11,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2475a25-97c4-40cb-854d-37839f437dcc/dqc_reference/checkm_data
[2024-01-24 14:39:11,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:11,949] [INFO] Task started: CheckM
[2024-01-24 14:39:11,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987175.1_ASM398717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987175.1_ASM398717v1_genomic.fna/checkm_input GCF_003987175.1_ASM398717v1_genomic.fna/checkm_result
[2024-01-24 14:39:42,523] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:42,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:42,545] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:42,546] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:42,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987175.1_ASM398717v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:42,547] [INFO] Task started: Blastn
[2024-01-24 14:39:42,547] [INFO] Running command: blastn -query GCF_003987175.1_ASM398717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2475a25-97c4-40cb-854d-37839f437dcc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987175.1_ASM398717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:43,726] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:43,729] [INFO] Selected 23 target genomes.
[2024-01-24 14:39:43,730] [INFO] Target genome list was writen to GCF_003987175.1_ASM398717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:43,745] [INFO] Task started: fastANI
[2024-01-24 14:39:43,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgb17a80b7-a42a-4c43-bd6f-1575501245a5/GCF_003987175.1_ASM398717v1_genomic.fna.gz --refList GCF_003987175.1_ASM398717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987175.1_ASM398717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:56,307] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:56,320] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:56,320] [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_003987175.1	s__Aliidiomarina sanyensis	100.0	842	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003987315.1	s__Aliidiomarina haloalkalitolerans	79.2134	142	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354615.1	s__Aliidiomarina sp015354615	79.0961	223	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007096385.1	s__Aliidiomarina sp007096385	78.7782	226	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987345.1	s__Aliidiomarina shirensis	78.5879	123	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.30	99.30	0.95	0.95	2	-
GCF_003987335.1	s__Aliidiomarina maris	78.5477	84	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.15	98.30	0.97	0.95	3	-
GCF_003987045.1	s__Pseudidiomarina marina	78.3938	62	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	78.1189	57	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003986955.1	s__Aliidiomarina sedimenti	78.0039	68	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	77.8712	52	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	77.721	55	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753735.1	s__Pseudidiomarina atlantica	77.6363	53	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:56,324] [INFO] GTDB search result was written to GCF_003987175.1_ASM398717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:56,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:56,329] [INFO] DFAST_QC result json was written to GCF_003987175.1_ASM398717v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:56,329] [INFO] DFAST_QC completed!
[2024-01-24 14:39:56,329] [INFO] Total running time: 0h1m11s