[2024-01-24 13:58:10,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,228] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,228] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd2dbd9e-54d3-49b2-9e7c-b0aaf0e847cf/dqc_reference
[2024-01-24 13:58:11,325] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,325] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg705569b6-f898-488c-b50c-76406866dff5/GCF_003316875.1_ASM331687v1_genomic.fna.gz | prodigal -d GCF_003316875.1_ASM331687v1_genomic.fna/cds.fna -a GCF_003316875.1_ASM331687v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:18,026] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:18,026] [INFO] Task started: HMMsearch
[2024-01-24 13:58:18,026] [INFO] Running command: hmmsearch --tblout GCF_003316875.1_ASM331687v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd2dbd9e-54d3-49b2-9e7c-b0aaf0e847cf/dqc_reference/reference_markers.hmm GCF_003316875.1_ASM331687v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:18,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:18,214] [INFO] Found 6/6 markers.
[2024-01-24 13:58:18,237] [INFO] Query marker FASTA was written to GCF_003316875.1_ASM331687v1_genomic.fna/markers.fasta
[2024-01-24 13:58:18,237] [INFO] Task started: Blastn
[2024-01-24 13:58:18,237] [INFO] Running command: blastn -query GCF_003316875.1_ASM331687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd2dbd9e-54d3-49b2-9e7c-b0aaf0e847cf/dqc_reference/reference_markers.fasta -out GCF_003316875.1_ASM331687v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:18,859] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:18,862] [INFO] Selected 27 target genomes.
[2024-01-24 13:58:18,862] [INFO] Target genome list was writen to GCF_003316875.1_ASM331687v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:18,922] [INFO] Task started: fastANI
[2024-01-24 13:58:18,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg705569b6-f898-488c-b50c-76406866dff5/GCF_003316875.1_ASM331687v1_genomic.fna.gz --refList GCF_003316875.1_ASM331687v1_genomic.fna/target_genomes.txt --output GCF_003316875.1_ASM331687v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:32,083] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:32,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd2dbd9e-54d3-49b2-9e7c-b0aaf0e847cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:32,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd2dbd9e-54d3-49b2-9e7c-b0aaf0e847cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:32,092] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:32,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:32,092] [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 celeris	strain=F3105	GCA_003316875.1	2249428	2249428	type	True	100.0	921	922	95	conclusive
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	78.4382	53	922	95	below_threshold
Aliidiomarina taiwanensis	strain=AIT1	GCA_003987015.1	946228	946228	type	True	78.4252	157	922	95	below_threshold
Aliidiomarina haloalkalitolerans	strain=AK5	GCA_003987315.1	859059	859059	type	True	78.3993	122	922	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	78.2094	58	922	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	78.1616	103	922	95	below_threshold
Aliidiomarina shirensis	strain=AIS	GCA_003987345.1	1048642	1048642	type	True	78.0667	86	922	95	below_threshold
Aliidiomarina soli	strain=Y4G10-17	GCA_003986975.1	1928574	1928574	type	True	77.999	75	922	95	below_threshold
Pseudidiomarina insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	77.9513	52	922	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	77.8994	116	922	95	below_threshold
Aliidiomarina minuta	strain=MLST1	GCA_003987145.1	880057	880057	type	True	77.7063	72	922	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	77.5755	77	922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:32,093] [INFO] DFAST Taxonomy check result was written to GCF_003316875.1_ASM331687v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:32,094] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:32,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:32,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd2dbd9e-54d3-49b2-9e7c-b0aaf0e847cf/dqc_reference/checkm_data
[2024-01-24 13:58:32,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:32,123] [INFO] Task started: CheckM
[2024-01-24 13:58:32,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003316875.1_ASM331687v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003316875.1_ASM331687v1_genomic.fna/checkm_input GCF_003316875.1_ASM331687v1_genomic.fna/checkm_result
[2024-01-24 13:58:55,394] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:55,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:55,410] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:55,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:55,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003316875.1_ASM331687v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:55,411] [INFO] Task started: Blastn
[2024-01-24 13:58:55,411] [INFO] Running command: blastn -query GCF_003316875.1_ASM331687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd2dbd9e-54d3-49b2-9e7c-b0aaf0e847cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_003316875.1_ASM331687v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:56,411] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:56,414] [INFO] Selected 26 target genomes.
[2024-01-24 13:58:56,414] [INFO] Target genome list was writen to GCF_003316875.1_ASM331687v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:56,428] [INFO] Task started: fastANI
[2024-01-24 13:58:56,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg705569b6-f898-488c-b50c-76406866dff5/GCF_003316875.1_ASM331687v1_genomic.fna.gz --refList GCF_003316875.1_ASM331687v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003316875.1_ASM331687v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:09,160] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:09,169] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:09,170] [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_003316875.1	s__Aliidiomarina celeris	100.0	921	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001458075.1	s__Aliidiomarina sp001458075	78.8733	138	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003290085.1	s__Aliidiomarina sp003290085	78.4704	149	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987315.1	s__Aliidiomarina haloalkalitolerans	78.4115	121	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987015.1	s__Aliidiomarina taiwanensis	78.4095	157	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	78.2094	58	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987345.1	s__Aliidiomarina shirensis	78.0539	86	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.30	99.30	0.95	0.95	2	-
GCF_003986975.1	s__Aliidiomarina soli	77.9861	74	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_000218785.1	s__Aliidiomarina sp000218785	77.9759	100	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	77.971	51	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007096385.1	s__Aliidiomarina sp007096385	77.9603	119	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003986955.1	s__Aliidiomarina sedimenti	77.7122	74	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_003999375.1	s__Pseudidiomarina mangrovi	77.7118	87	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002808045.1	s__Idiomarina sp002808045	77.36	66	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCF_900177775.1	s__Pseudidiomarina planktonica	77.2166	67	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:09,171] [INFO] GTDB search result was written to GCF_003316875.1_ASM331687v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:09,172] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:09,175] [INFO] DFAST_QC result json was written to GCF_003316875.1_ASM331687v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:09,175] [INFO] DFAST_QC completed!
[2024-01-24 13:59:09,175] [INFO] Total running time: 0h0m59s