[2023-06-28 18:45:50,800] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:45:50,805] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:45:50,805] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd28467f-126d-4e65-9a10-a50364a37b09/dqc_reference
[2023-06-28 18:45:52,125] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:45:52,126] [INFO] Task started: Prodigal
[2023-06-28 18:45:52,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg18f8bb36-9f3c-4ce0-a8df-ebd4cb1a2b39/GCA_020201175.1_ASM2020117v1_genomic.fna.gz | prodigal -d GCA_020201175.1_ASM2020117v1_genomic.fna/cds.fna -a GCA_020201175.1_ASM2020117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:45:55,095] [INFO] Task succeeded: Prodigal
[2023-06-28 18:45:55,095] [INFO] Task started: HMMsearch
[2023-06-28 18:45:55,095] [INFO] Running command: hmmsearch --tblout GCA_020201175.1_ASM2020117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd28467f-126d-4e65-9a10-a50364a37b09/dqc_reference/reference_markers.hmm GCA_020201175.1_ASM2020117v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:45:55,296] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:45:55,297] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg18f8bb36-9f3c-4ce0-a8df-ebd4cb1a2b39/GCA_020201175.1_ASM2020117v1_genomic.fna.gz]
[2023-06-28 18:45:55,319] [INFO] Query marker FASTA was written to GCA_020201175.1_ASM2020117v1_genomic.fna/markers.fasta
[2023-06-28 18:45:55,319] [INFO] Task started: Blastn
[2023-06-28 18:45:55,319] [INFO] Running command: blastn -query GCA_020201175.1_ASM2020117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd28467f-126d-4e65-9a10-a50364a37b09/dqc_reference/reference_markers.fasta -out GCA_020201175.1_ASM2020117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:45:55,943] [INFO] Task succeeded: Blastn
[2023-06-28 18:45:55,947] [INFO] Selected 21 target genomes.
[2023-06-28 18:45:55,947] [INFO] Target genome list was writen to GCA_020201175.1_ASM2020117v1_genomic.fna/target_genomes.txt
[2023-06-28 18:45:55,950] [INFO] Task started: fastANI
[2023-06-28 18:45:55,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg18f8bb36-9f3c-4ce0-a8df-ebd4cb1a2b39/GCA_020201175.1_ASM2020117v1_genomic.fna.gz --refList GCA_020201175.1_ASM2020117v1_genomic.fna/target_genomes.txt --output GCA_020201175.1_ASM2020117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:46:07,135] [INFO] Task succeeded: fastANI
[2023-06-28 18:46:07,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd28467f-126d-4e65-9a10-a50364a37b09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:46:07,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd28467f-126d-4e65-9a10-a50364a37b09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:46:07,145] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:46:07,145] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:46:07,145] [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
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	84.7163	260	291	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	83.5988	252	291	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	83.5517	250	291	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	83.1366	243	291	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	80.0981	138	291	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	80.09	139	291	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	79.7225	150	291	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	79.0494	71	291	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:46:07,148] [INFO] DFAST Taxonomy check result was written to GCA_020201175.1_ASM2020117v1_genomic.fna/tc_result.tsv
[2023-06-28 18:46:07,148] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:46:07,149] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:46:07,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd28467f-126d-4e65-9a10-a50364a37b09/dqc_reference/checkm_data
[2023-06-28 18:46:07,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:46:07,175] [INFO] Task started: CheckM
[2023-06-28 18:46:07,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020201175.1_ASM2020117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020201175.1_ASM2020117v1_genomic.fna/checkm_input GCA_020201175.1_ASM2020117v1_genomic.fna/checkm_result
[2023-06-28 18:46:25,651] [INFO] Task succeeded: CheckM
[2023-06-28 18:46:25,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.37%
Contamintation: 12.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:46:25,680] [INFO] ===== Completeness check finished =====
[2023-06-28 18:46:25,680] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:46:25,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020201175.1_ASM2020117v1_genomic.fna/markers.fasta)
[2023-06-28 18:46:25,681] [INFO] Task started: Blastn
[2023-06-28 18:46:25,681] [INFO] Running command: blastn -query GCA_020201175.1_ASM2020117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd28467f-126d-4e65-9a10-a50364a37b09/dqc_reference/reference_markers_gtdb.fasta -out GCA_020201175.1_ASM2020117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:46:26,497] [INFO] Task succeeded: Blastn
[2023-06-28 18:46:26,502] [INFO] Selected 19 target genomes.
[2023-06-28 18:46:26,503] [INFO] Target genome list was writen to GCA_020201175.1_ASM2020117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:46:26,558] [INFO] Task started: fastANI
[2023-06-28 18:46:26,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg18f8bb36-9f3c-4ce0-a8df-ebd4cb1a2b39/GCA_020201175.1_ASM2020117v1_genomic.fna.gz --refList GCA_020201175.1_ASM2020117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020201175.1_ASM2020117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:46:36,469] [INFO] Task succeeded: fastANI
[2023-06-28 18:46:36,478] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:46:36,479] [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_003987255.1	s__Idiomarina ramblicola	84.7163	260	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116625.1	s__Idiomarina abyssalis	83.5988	252	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
GCF_000008465.1	s__Idiomarina loihiensis	83.1366	243	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_900100855.1	s__Idiomarina zobellii	80.09	139	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_002808045.1	s__Idiomarina sp002808045	80.049	142	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	79.997	144	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_003987095.1	s__Idiomarina piscisalsi	79.7225	150	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987275.1	s__Idiomarina seosinensis	79.7091	64	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362895.1	s__Idiomarina sp002729675	79.3178	69	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_003987185.1	s__Idiomarina aquatica	79.0494	71	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-28 18:46:36,481] [INFO] GTDB search result was written to GCA_020201175.1_ASM2020117v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:46:36,481] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:46:36,485] [INFO] DFAST_QC result json was written to GCA_020201175.1_ASM2020117v1_genomic.fna/dqc_result.json
[2023-06-28 18:46:36,485] [INFO] DFAST_QC completed!
[2023-06-28 18:46:36,485] [INFO] Total running time: 0h0m46s