[2024-01-25 20:23:35,616] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:35,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:35,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg02393308-fcef-44cd-bc06-c33bf8128bad/dqc_reference
[2024-01-25 20:23:36,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:36,701] [INFO] Task started: Prodigal
[2024-01-25 20:23:36,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg605d18a5-0498-46c6-b68c-0931ed1a10bf/GCF_015354615.1_ASM1535461v1_genomic.fna.gz | prodigal -d GCF_015354615.1_ASM1535461v1_genomic.fna/cds.fna -a GCF_015354615.1_ASM1535461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:43,124] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:43,125] [INFO] Task started: HMMsearch
[2024-01-25 20:23:43,125] [INFO] Running command: hmmsearch --tblout GCF_015354615.1_ASM1535461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02393308-fcef-44cd-bc06-c33bf8128bad/dqc_reference/reference_markers.hmm GCF_015354615.1_ASM1535461v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:43,327] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:43,328] [INFO] Found 6/6 markers.
[2024-01-25 20:23:43,351] [INFO] Query marker FASTA was written to GCF_015354615.1_ASM1535461v1_genomic.fna/markers.fasta
[2024-01-25 20:23:43,351] [INFO] Task started: Blastn
[2024-01-25 20:23:43,351] [INFO] Running command: blastn -query GCF_015354615.1_ASM1535461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02393308-fcef-44cd-bc06-c33bf8128bad/dqc_reference/reference_markers.fasta -out GCF_015354615.1_ASM1535461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:44,011] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:44,013] [INFO] Selected 21 target genomes.
[2024-01-25 20:23:44,014] [INFO] Target genome list was writen to GCF_015354615.1_ASM1535461v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:44,037] [INFO] Task started: fastANI
[2024-01-25 20:23:44,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg605d18a5-0498-46c6-b68c-0931ed1a10bf/GCF_015354615.1_ASM1535461v1_genomic.fna.gz --refList GCF_015354615.1_ASM1535461v1_genomic.fna/target_genomes.txt --output GCF_015354615.1_ASM1535461v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:57,578] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:57,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02393308-fcef-44cd-bc06-c33bf8128bad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:57,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02393308-fcef-44cd-bc06-c33bf8128bad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:57,586] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:57,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:57,586] [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 indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	100.0	873	874	95	conclusive
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	81.5074	499	874	95	below_threshold
Aliidiomarina sanyensis	strain=GYP-17	GCA_003987175.1	1249555	1249555	type	True	79.193	228	874	95	below_threshold
Aliidiomarina shirensis	strain=AIS	GCA_003987345.1	1048642	1048642	type	True	78.5205	140	874	95	below_threshold
Aliidiomarina iranensis	strain=GBPy7	GCA_003987135.1	1434071	1434071	type	True	78.2904	150	874	95	below_threshold
Aliidiomarina haloalkalitolerans	strain=AK5	GCA_003987315.1	859059	859059	type	True	78.2373	174	874	95	below_threshold
Aliidiomarina maris	strain=CF12-14	GCA_003987335.1	531312	531312	type	True	77.5058	89	874	95	below_threshold
Aliidiomarina minuta	strain=MLST1	GCA_003987145.1	880057	880057	type	True	77.423	67	874	95	below_threshold
Pseudidiomarina atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	77.3417	60	874	95	below_threshold
Idiomarina xiamenensis	strain=10-D-4	GCA_000299895.1	1207041	1207041	type	True	77.0344	61	874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:57,587] [INFO] DFAST Taxonomy check result was written to GCF_015354615.1_ASM1535461v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:57,588] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:57,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:57,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02393308-fcef-44cd-bc06-c33bf8128bad/dqc_reference/checkm_data
[2024-01-25 20:23:57,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:57,616] [INFO] Task started: CheckM
[2024-01-25 20:23:57,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015354615.1_ASM1535461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015354615.1_ASM1535461v1_genomic.fna/checkm_input GCF_015354615.1_ASM1535461v1_genomic.fna/checkm_result
[2024-01-25 20:24:21,737] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:21,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:21,769] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:21,769] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:21,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015354615.1_ASM1535461v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:21,772] [INFO] Task started: Blastn
[2024-01-25 20:24:21,772] [INFO] Running command: blastn -query GCF_015354615.1_ASM1535461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02393308-fcef-44cd-bc06-c33bf8128bad/dqc_reference/reference_markers_gtdb.fasta -out GCF_015354615.1_ASM1535461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:22,866] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:22,871] [INFO] Selected 21 target genomes.
[2024-01-25 20:24:22,872] [INFO] Target genome list was writen to GCF_015354615.1_ASM1535461v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:22,906] [INFO] Task started: fastANI
[2024-01-25 20:24:22,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg605d18a5-0498-46c6-b68c-0931ed1a10bf/GCF_015354615.1_ASM1535461v1_genomic.fna.gz --refList GCF_015354615.1_ASM1535461v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015354615.1_ASM1535461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:34,866] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:34,873] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:34,873] [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_015354615.1	s__Aliidiomarina sp015354615	100.0	873	874	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_007096385.1	s__Aliidiomarina sp007096385	81.5336	497	874	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	79.1646	230	874	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	78.5296	139	874	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	78.308	150	874	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	78.2373	174	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001458075.1	s__Aliidiomarina sp001458075	78.0388	80	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000753735.1	s__Pseudidiomarina atlantica	77.2967	61	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182315.1	s__Pseudidiomarina maritima_A	77.2768	68	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	98.70	97.84	0.93	0.89	6	-
GCF_000299895.1	s__Idiomarina xiamenensis	77.0344	61	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:34,879] [INFO] GTDB search result was written to GCF_015354615.1_ASM1535461v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:34,879] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:34,882] [INFO] DFAST_QC result json was written to GCF_015354615.1_ASM1535461v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:34,882] [INFO] DFAST_QC completed!
[2024-01-25 20:24:34,882] [INFO] Total running time: 0h0m59s