[2024-01-24 14:05:32,589] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:32,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:32,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg81790870-18fc-40e9-9905-4027049e7fa6/dqc_reference
[2024-01-24 14:05:33,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:33,895] [INFO] Task started: Prodigal
[2024-01-24 14:05:33,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgab41e4bf-15da-4774-a912-2808b77a0e3e/GCF_003987015.1_ASM398701v1_genomic.fna.gz | prodigal -d GCF_003987015.1_ASM398701v1_genomic.fna/cds.fna -a GCF_003987015.1_ASM398701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:40,870] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:40,870] [INFO] Task started: HMMsearch
[2024-01-24 14:05:40,870] [INFO] Running command: hmmsearch --tblout GCF_003987015.1_ASM398701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81790870-18fc-40e9-9905-4027049e7fa6/dqc_reference/reference_markers.hmm GCF_003987015.1_ASM398701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:41,099] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:41,100] [INFO] Found 6/6 markers.
[2024-01-24 14:05:41,125] [INFO] Query marker FASTA was written to GCF_003987015.1_ASM398701v1_genomic.fna/markers.fasta
[2024-01-24 14:05:41,125] [INFO] Task started: Blastn
[2024-01-24 14:05:41,125] [INFO] Running command: blastn -query GCF_003987015.1_ASM398701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81790870-18fc-40e9-9905-4027049e7fa6/dqc_reference/reference_markers.fasta -out GCF_003987015.1_ASM398701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:41,908] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:41,912] [INFO] Selected 27 target genomes.
[2024-01-24 14:05:41,912] [INFO] Target genome list was writen to GCF_003987015.1_ASM398701v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:41,937] [INFO] Task started: fastANI
[2024-01-24 14:05:41,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgab41e4bf-15da-4774-a912-2808b77a0e3e/GCF_003987015.1_ASM398701v1_genomic.fna.gz --refList GCF_003987015.1_ASM398701v1_genomic.fna/target_genomes.txt --output GCF_003987015.1_ASM398701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:57,110] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:57,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81790870-18fc-40e9-9905-4027049e7fa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:57,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81790870-18fc-40e9-9905-4027049e7fa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:57,120] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:57,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:57,121] [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 taiwanensis	strain=AIT1	GCA_003987015.1	946228	946228	type	True	100.0	826	828	95	conclusive
Aliidiomarina celeris	strain=F3105	GCA_003316875.1	2249428	2249428	type	True	78.4593	158	828	95	below_threshold
Aliidiomarina shirensis	strain=AIS	GCA_003987345.1	1048642	1048642	type	True	78.2438	86	828	95	below_threshold
Aliidiomarina haloalkalitolerans	strain=AK5	GCA_003987315.1	859059	859059	type	True	77.83	92	828	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	77.6772	85	828	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	77.5816	77	828	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	77.5451	63	828	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	77.5016	62	828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:57,122] [INFO] DFAST Taxonomy check result was written to GCF_003987015.1_ASM398701v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:57,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:57,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:57,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81790870-18fc-40e9-9905-4027049e7fa6/dqc_reference/checkm_data
[2024-01-24 14:05:57,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:57,154] [INFO] Task started: CheckM
[2024-01-24 14:05:57,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987015.1_ASM398701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987015.1_ASM398701v1_genomic.fna/checkm_input GCF_003987015.1_ASM398701v1_genomic.fna/checkm_result
[2024-01-24 14:06:22,243] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:22,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:22,261] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:22,261] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:22,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987015.1_ASM398701v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:22,262] [INFO] Task started: Blastn
[2024-01-24 14:06:22,262] [INFO] Running command: blastn -query GCF_003987015.1_ASM398701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81790870-18fc-40e9-9905-4027049e7fa6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987015.1_ASM398701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:23,354] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:23,357] [INFO] Selected 25 target genomes.
[2024-01-24 14:06:23,358] [INFO] Target genome list was writen to GCF_003987015.1_ASM398701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:23,377] [INFO] Task started: fastANI
[2024-01-24 14:06:23,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgab41e4bf-15da-4774-a912-2808b77a0e3e/GCF_003987015.1_ASM398701v1_genomic.fna.gz --refList GCF_003987015.1_ASM398701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987015.1_ASM398701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:37,796] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:37,805] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:37,805] [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_003987015.1	s__Aliidiomarina taiwanensis	100.0	826	828	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_003316875.1	s__Aliidiomarina celeris	78.4844	157	828	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	78.2438	86	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.30	99.30	0.95	0.95	2	-
GCF_003290085.1	s__Aliidiomarina sp003290085	78.0769	100	828	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	77.8419	91	828	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	77.6576	83	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218785.1	s__Aliidiomarina sp000218785	77.6015	69	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418345.1	s__Pseudidiomarina woesei	77.5451	63	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	77.3523	62	828	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 14:06:37,807] [INFO] GTDB search result was written to GCF_003987015.1_ASM398701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:37,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:37,810] [INFO] DFAST_QC result json was written to GCF_003987015.1_ASM398701v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:37,811] [INFO] DFAST_QC completed!
[2024-01-24 14:06:37,811] [INFO] Total running time: 0h1m5s