[2024-01-24 11:35:23,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg55a05474-e08d-49f2-adcd-d4f287be3638/dqc_reference
[2024-01-24 11:35:26,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,242] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg079e8c73-f2d7-482b-935e-2752fe301444/GCF_003987335.1_ASM398733v1_genomic.fna.gz | prodigal -d GCF_003987335.1_ASM398733v1_genomic.fna/cds.fna -a GCF_003987335.1_ASM398733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:34,566] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:34,567] [INFO] Task started: HMMsearch
[2024-01-24 11:35:34,567] [INFO] Running command: hmmsearch --tblout GCF_003987335.1_ASM398733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55a05474-e08d-49f2-adcd-d4f287be3638/dqc_reference/reference_markers.hmm GCF_003987335.1_ASM398733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:34,872] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:34,874] [INFO] Found 6/6 markers.
[2024-01-24 11:35:34,907] [INFO] Query marker FASTA was written to GCF_003987335.1_ASM398733v1_genomic.fna/markers.fasta
[2024-01-24 11:35:34,908] [INFO] Task started: Blastn
[2024-01-24 11:35:34,908] [INFO] Running command: blastn -query GCF_003987335.1_ASM398733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55a05474-e08d-49f2-adcd-d4f287be3638/dqc_reference/reference_markers.fasta -out GCF_003987335.1_ASM398733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:35,670] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:35,674] [INFO] Selected 26 target genomes.
[2024-01-24 11:35:35,674] [INFO] Target genome list was writen to GCF_003987335.1_ASM398733v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:35,694] [INFO] Task started: fastANI
[2024-01-24 11:35:35,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg079e8c73-f2d7-482b-935e-2752fe301444/GCF_003987335.1_ASM398733v1_genomic.fna.gz --refList GCF_003987335.1_ASM398733v1_genomic.fna/target_genomes.txt --output GCF_003987335.1_ASM398733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:50,446] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:50,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55a05474-e08d-49f2-adcd-d4f287be3638/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:50,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55a05474-e08d-49f2-adcd-d4f287be3638/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:50,459] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:50,459] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:50,459] [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 maris	strain=CF12-14	GCA_003987335.1	531312	531312	type	True	100.0	980	982	95	conclusive
Aliidiomarina soli	strain=Y4G10-17	GCA_003986975.1	1928574	1928574	type	True	78.9751	212	982	95	below_threshold
Aliidiomarina sedimenti	strain=GBSy1	GCA_003986955.1	1933879	1933879	type	True	78.8443	221	982	95	below_threshold
Aliidiomarina celeris	strain=F3105	GCA_003316875.1	2249428	2249428	type	True	78.4741	103	982	95	below_threshold
Aliidiomarina minuta	strain=MLST1	GCA_003987145.1	880057	880057	type	True	78.2392	146	982	95	below_threshold
Aliidiomarina iranensis	strain=GBPy7	GCA_003987135.1	1434071	1434071	type	True	77.9433	77	982	95	below_threshold
Aliidiomarina shirensis	strain=AIS	GCA_003987345.1	1048642	1048642	type	True	77.9361	74	982	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	77.8884	86	982	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	77.5983	91	982	95	below_threshold
Idiomarina xiamenensis	strain=10-D-4	GCA_000299895.1	1207041	1207041	type	True	77.408	68	982	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	77.3169	67	982	95	below_threshold
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	77.2318	51	982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:50,461] [INFO] DFAST Taxonomy check result was written to GCF_003987335.1_ASM398733v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:50,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:50,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:50,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55a05474-e08d-49f2-adcd-d4f287be3638/dqc_reference/checkm_data
[2024-01-24 11:35:50,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:50,496] [INFO] Task started: CheckM
[2024-01-24 11:35:50,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987335.1_ASM398733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987335.1_ASM398733v1_genomic.fna/checkm_input GCF_003987335.1_ASM398733v1_genomic.fna/checkm_result
[2024-01-24 11:36:20,995] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:20,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:21,017] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:21,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:21,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987335.1_ASM398733v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:21,019] [INFO] Task started: Blastn
[2024-01-24 11:36:21,019] [INFO] Running command: blastn -query GCF_003987335.1_ASM398733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55a05474-e08d-49f2-adcd-d4f287be3638/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987335.1_ASM398733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:22,185] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:22,189] [INFO] Selected 24 target genomes.
[2024-01-24 11:36:22,189] [INFO] Target genome list was writen to GCF_003987335.1_ASM398733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:22,206] [INFO] Task started: fastANI
[2024-01-24 11:36:22,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg079e8c73-f2d7-482b-935e-2752fe301444/GCF_003987335.1_ASM398733v1_genomic.fna.gz --refList GCF_003987335.1_ASM398733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987335.1_ASM398733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:33,743] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:33,760] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:33,761] [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_003987335.1	s__Aliidiomarina maris	100.0	980	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.15	98.30	0.97	0.95	3	conclusive
GCF_003986975.1	s__Aliidiomarina soli	78.9807	213	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_003986955.1	s__Aliidiomarina sedimenti	78.8443	221	982	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	78.5463	71	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316875.1	s__Aliidiomarina celeris	78.4704	102	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987175.1	s__Aliidiomarina sanyensis	78.4509	83	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987145.1	s__Aliidiomarina minuta	78.213	147	982	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	77.9361	74	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.30	99.30	0.95	0.95	2	-
GCF_003987135.1	s__Aliidiomarina iranensis	77.898	78	982	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	77.897	85	982	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	77.6032	90	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299895.1	s__Idiomarina xiamenensis	77.408	68	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002808045.1	s__Idiomarina sp002808045	77.3527	64	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCF_000008465.1	s__Idiomarina loihiensis	77.3194	66	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	77.277	63	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_003987255.1	s__Idiomarina ramblicola	77.2318	51	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	77.0692	79	982	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 11:36:33,762] [INFO] GTDB search result was written to GCF_003987335.1_ASM398733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:33,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:33,766] [INFO] DFAST_QC result json was written to GCF_003987335.1_ASM398733v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:33,767] [INFO] DFAST_QC completed!
[2024-01-24 11:36:33,767] [INFO] Total running time: 0h1m11s