[2024-01-24 15:03:29,340] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:29,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:29,343] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c0da8f0-e760-4f29-9a60-f5e68a67b5a6/dqc_reference
[2024-01-24 15:03:32,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:32,683] [INFO] Task started: Prodigal
[2024-01-24 15:03:32,684] [INFO] Running command: gunzip -c /var/lib/cwl/stgad6a24d9-367c-4280-8122-cc5cb9cded21/GCF_003987145.1_ASM398714v1_genomic.fna.gz | prodigal -d GCF_003987145.1_ASM398714v1_genomic.fna/cds.fna -a GCF_003987145.1_ASM398714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:39,052] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:39,053] [INFO] Task started: HMMsearch
[2024-01-24 15:03:39,053] [INFO] Running command: hmmsearch --tblout GCF_003987145.1_ASM398714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c0da8f0-e760-4f29-9a60-f5e68a67b5a6/dqc_reference/reference_markers.hmm GCF_003987145.1_ASM398714v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:39,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:39,257] [INFO] Found 6/6 markers.
[2024-01-24 15:03:39,280] [INFO] Query marker FASTA was written to GCF_003987145.1_ASM398714v1_genomic.fna/markers.fasta
[2024-01-24 15:03:39,281] [INFO] Task started: Blastn
[2024-01-24 15:03:39,281] [INFO] Running command: blastn -query GCF_003987145.1_ASM398714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c0da8f0-e760-4f29-9a60-f5e68a67b5a6/dqc_reference/reference_markers.fasta -out GCF_003987145.1_ASM398714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:39,965] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:39,967] [INFO] Selected 24 target genomes.
[2024-01-24 15:03:39,968] [INFO] Target genome list was writen to GCF_003987145.1_ASM398714v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:39,974] [INFO] Task started: fastANI
[2024-01-24 15:03:39,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgad6a24d9-367c-4280-8122-cc5cb9cded21/GCF_003987145.1_ASM398714v1_genomic.fna.gz --refList GCF_003987145.1_ASM398714v1_genomic.fna/target_genomes.txt --output GCF_003987145.1_ASM398714v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:53,362] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:53,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c0da8f0-e760-4f29-9a60-f5e68a67b5a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:53,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c0da8f0-e760-4f29-9a60-f5e68a67b5a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:53,371] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:53,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:53,372] [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 minuta	strain=MLST1	GCA_003987145.1	880057	880057	type	True	100.0	983	983	95	conclusive
Aliidiomarina soli	strain=Y4G10-17	GCA_003986975.1	1928574	1928574	type	True	78.63	209	983	95	below_threshold
Aliidiomarina maris	strain=CF12-14	GCA_003987335.1	531312	531312	type	True	78.3562	142	983	95	below_threshold
Aliidiomarina sedimenti	strain=GBSy1	GCA_003986955.1	1933879	1933879	type	True	78.3125	216	983	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	77.7644	58	983	95	below_threshold
Pseudidiomarina insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	77.6488	51	983	95	below_threshold
Aliidiomarina haloalkalitolerans	strain=AK5	GCA_003987315.1	859059	859059	type	True	77.5906	74	983	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	77.3528	69	983	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	77.3525	61	983	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	77.2363	68	983	95	below_threshold
Pseudidiomarina atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	76.6497	51	983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:53,373] [INFO] DFAST Taxonomy check result was written to GCF_003987145.1_ASM398714v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:53,373] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:53,373] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:53,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c0da8f0-e760-4f29-9a60-f5e68a67b5a6/dqc_reference/checkm_data
[2024-01-24 15:03:53,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:53,405] [INFO] Task started: CheckM
[2024-01-24 15:03:53,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987145.1_ASM398714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987145.1_ASM398714v1_genomic.fna/checkm_input GCF_003987145.1_ASM398714v1_genomic.fna/checkm_result
[2024-01-24 15:04:16,473] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:16,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:16,489] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:16,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:16,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987145.1_ASM398714v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:16,490] [INFO] Task started: Blastn
[2024-01-24 15:04:16,490] [INFO] Running command: blastn -query GCF_003987145.1_ASM398714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c0da8f0-e760-4f29-9a60-f5e68a67b5a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987145.1_ASM398714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:17,546] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:17,549] [INFO] Selected 21 target genomes.
[2024-01-24 15:04:17,549] [INFO] Target genome list was writen to GCF_003987145.1_ASM398714v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:17,559] [INFO] Task started: fastANI
[2024-01-24 15:04:17,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgad6a24d9-367c-4280-8122-cc5cb9cded21/GCF_003987145.1_ASM398714v1_genomic.fna.gz --refList GCF_003987145.1_ASM398714v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987145.1_ASM398714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:29,494] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:29,502] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:29,502] [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_003987145.1	s__Aliidiomarina minuta	100.0	983	983	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_003986975.1	s__Aliidiomarina soli	78.6354	207	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_003987335.1	s__Aliidiomarina maris	78.3562	142	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.15	98.30	0.97	0.95	3	-
GCF_003986955.1	s__Aliidiomarina sedimenti	78.3089	215	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_015354615.1	s__Aliidiomarina sp015354615	77.7644	58	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987135.1	s__Aliidiomarina iranensis	77.6633	69	983	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	77.5906	74	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316875.1	s__Aliidiomarina celeris	77.2958	79	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753715.1	s__Pseudidiomarina salinarum	77.259	62	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100855.1	s__Idiomarina zobellii	77.2363	68	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_003584565.2	s__Alteromonas sp002729795	76.7224	51	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_000753735.1	s__Pseudidiomarina atlantica	76.6966	52	983	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 15:04:29,503] [INFO] GTDB search result was written to GCF_003987145.1_ASM398714v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:29,504] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:29,506] [INFO] DFAST_QC result json was written to GCF_003987145.1_ASM398714v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:29,507] [INFO] DFAST_QC completed!
[2024-01-24 15:04:29,507] [INFO] Total running time: 0h1m0s