[2024-01-24 13:56:12,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:12,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:12,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg23960296-72fb-45a1-ac5f-64421ee5e169/dqc_reference
[2024-01-24 13:56:14,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,420] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,420] [INFO] Running command: gunzip -c /var/lib/cwl/stg0104607e-6368-4171-b59d-b26ee676d16c/GCF_007096385.1_ASM709638v1_genomic.fna.gz | prodigal -d GCF_007096385.1_ASM709638v1_genomic.fna/cds.fna -a GCF_007096385.1_ASM709638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:21,738] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:21,738] [INFO] Task started: HMMsearch
[2024-01-24 13:56:21,738] [INFO] Running command: hmmsearch --tblout GCF_007096385.1_ASM709638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23960296-72fb-45a1-ac5f-64421ee5e169/dqc_reference/reference_markers.hmm GCF_007096385.1_ASM709638v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:22,006] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:22,008] [INFO] Found 6/6 markers.
[2024-01-24 13:56:22,038] [INFO] Query marker FASTA was written to GCF_007096385.1_ASM709638v1_genomic.fna/markers.fasta
[2024-01-24 13:56:22,038] [INFO] Task started: Blastn
[2024-01-24 13:56:22,039] [INFO] Running command: blastn -query GCF_007096385.1_ASM709638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23960296-72fb-45a1-ac5f-64421ee5e169/dqc_reference/reference_markers.fasta -out GCF_007096385.1_ASM709638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:22,979] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:22,983] [INFO] Selected 21 target genomes.
[2024-01-24 13:56:22,983] [INFO] Target genome list was writen to GCF_007096385.1_ASM709638v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:22,992] [INFO] Task started: fastANI
[2024-01-24 13:56:22,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg0104607e-6368-4171-b59d-b26ee676d16c/GCF_007096385.1_ASM709638v1_genomic.fna.gz --refList GCF_007096385.1_ASM709638v1_genomic.fna/target_genomes.txt --output GCF_007096385.1_ASM709638v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:35,674] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:35,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23960296-72fb-45a1-ac5f-64421ee5e169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:35,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23960296-72fb-45a1-ac5f-64421ee5e169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:35,690] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:35,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:35,691] [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 halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	100.0	851	852	95	conclusive
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	81.4778	514	852	95	below_threshold
Aliidiomarina sanyensis	strain=GYP-17	GCA_003987175.1	1249555	1249555	type	True	78.9105	225	852	95	below_threshold
Aliidiomarina haloalkalitolerans	strain=AK5	GCA_003987315.1	859059	859059	type	True	78.3127	161	852	95	below_threshold
Aliidiomarina shirensis	strain=AIS	GCA_003987345.1	1048642	1048642	type	True	78.2053	149	852	95	below_threshold
Aliidiomarina iranensis	strain=GBPy7	GCA_003987135.1	1434071	1434071	type	True	77.9786	139	852	95	below_threshold
Aliidiomarina soli	strain=Y4G10-17	GCA_003986975.1	1928574	1928574	type	True	77.5529	73	852	95	below_threshold
Aliidiomarina maris	strain=CF12-14	GCA_003987335.1	531312	531312	type	True	77.5378	94	852	95	below_threshold
Idiomarina tyrosinivorans	strain=CC-PW-9	GCA_003987475.1	1445662	1445662	type	True	77.2813	53	852	95	below_threshold
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	77.0876	66	852	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:35,692] [INFO] DFAST Taxonomy check result was written to GCF_007096385.1_ASM709638v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:35,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:35,693] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:35,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23960296-72fb-45a1-ac5f-64421ee5e169/dqc_reference/checkm_data
[2024-01-24 13:56:35,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:35,723] [INFO] Task started: CheckM
[2024-01-24 13:56:35,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007096385.1_ASM709638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007096385.1_ASM709638v1_genomic.fna/checkm_input GCF_007096385.1_ASM709638v1_genomic.fna/checkm_result
[2024-01-24 13:57:03,894] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:03,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:03,919] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:03,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:03,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007096385.1_ASM709638v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:03,920] [INFO] Task started: Blastn
[2024-01-24 13:57:03,920] [INFO] Running command: blastn -query GCF_007096385.1_ASM709638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23960296-72fb-45a1-ac5f-64421ee5e169/dqc_reference/reference_markers_gtdb.fasta -out GCF_007096385.1_ASM709638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:05,132] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:05,136] [INFO] Selected 19 target genomes.
[2024-01-24 13:57:05,136] [INFO] Target genome list was writen to GCF_007096385.1_ASM709638v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:05,152] [INFO] Task started: fastANI
[2024-01-24 13:57:05,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg0104607e-6368-4171-b59d-b26ee676d16c/GCF_007096385.1_ASM709638v1_genomic.fna.gz --refList GCF_007096385.1_ASM709638v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007096385.1_ASM709638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:16,257] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:16,271] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:16,271] [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_007096385.1	s__Aliidiomarina sp007096385	100.0	851	852	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_015354615.1	s__Aliidiomarina sp015354615	81.452	517	852	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	78.9289	224	852	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	78.5035	133	852	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	78.3064	162	852	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	77.9836	138	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987335.1	s__Aliidiomarina maris	77.55	95	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.15	98.30	0.97	0.95	3	-
GCF_003986975.1	s__Aliidiomarina soli	77.5377	75	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_000299895.1	s__Idiomarina xiamenensis	77.0912	52	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423165.1	s__Pseudidiomarina sediminum	77.0468	65	852	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 13:57:16,273] [INFO] GTDB search result was written to GCF_007096385.1_ASM709638v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:16,273] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:16,276] [INFO] DFAST_QC result json was written to GCF_007096385.1_ASM709638v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:16,276] [INFO] DFAST_QC completed!
[2024-01-24 13:57:16,277] [INFO] Total running time: 0h1m4s