[2024-01-24 13:55:17,577] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:17,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:17,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg54a37419-8cf5-48fa-8b24-21f1e37bda89/dqc_reference
[2024-01-24 13:55:18,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:18,878] [INFO] Task started: Prodigal
[2024-01-24 13:55:18,878] [INFO] Running command: gunzip -c /var/lib/cwl/stg338bf4b4-a04a-4971-8d7e-d0b1997bd838/GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna.gz | prodigal -d GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/cds.fna -a GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:25,843] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:25,843] [INFO] Task started: HMMsearch
[2024-01-24 13:55:25,843] [INFO] Running command: hmmsearch --tblout GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54a37419-8cf5-48fa-8b24-21f1e37bda89/dqc_reference/reference_markers.hmm GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:26,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:26,141] [INFO] Found 6/6 markers.
[2024-01-24 13:55:26,201] [INFO] Query marker FASTA was written to GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/markers.fasta
[2024-01-24 13:55:26,201] [INFO] Task started: Blastn
[2024-01-24 13:55:26,202] [INFO] Running command: blastn -query GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/markers.fasta -db /var/lib/cwl/stg54a37419-8cf5-48fa-8b24-21f1e37bda89/dqc_reference/reference_markers.fasta -out GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:27,012] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:27,015] [INFO] Selected 20 target genomes.
[2024-01-24 13:55:27,015] [INFO] Target genome list was writen to GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/target_genomes.txt
[2024-01-24 13:55:27,030] [INFO] Task started: fastANI
[2024-01-24 13:55:27,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg338bf4b4-a04a-4971-8d7e-d0b1997bd838/GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna.gz --refList GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/target_genomes.txt --output GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:39,919] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:39,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54a37419-8cf5-48fa-8b24-21f1e37bda89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:39,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54a37419-8cf5-48fa-8b24-21f1e37bda89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:39,932] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:39,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:39,933] [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
Pseudidiomarina piscicola	strain=CECT 9734	GCA_902806985.1	2614830	2614830	type	True	100.0	831	831	95	conclusive
Pseudidiomarina halophila	strain=BH195	GCA_003987215.1	1449799	1449799	type	True	80.3867	397	831	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	79.9214	185	831	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	79.6252	159	831	95	below_threshold
Pseudidiomarina homiensis	strain=PO-M2	GCA_003987225.1	364198	364198	type	True	79.5898	317	831	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	79.5833	186	831	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	79.583	186	831	95	below_threshold
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	79.5818	311	831	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	79.5681	178	831	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	79.3196	184	831	95	below_threshold
Pseudidiomarina sediminum	strain=c121	GCA_003987265.1	431675	431675	type	True	79.1659	253	831	95	below_threshold
Pseudidiomarina atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	79.1636	284	831	95	below_threshold
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	79.0165	251	831	95	below_threshold
Pseudidiomarina taiwanensis	strain=PIT1	GCA_003987435.1	337250	337250	type	True	78.9601	130	831	95	below_threshold
Pseudidiomarina aestuarii	strain=KYW314	GCA_003987355.1	624146	624146	suspected-type	True	78.5712	135	831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:39,941] [INFO] DFAST Taxonomy check result was written to GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/tc_result.tsv
[2024-01-24 13:55:39,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:39,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:39,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54a37419-8cf5-48fa-8b24-21f1e37bda89/dqc_reference/checkm_data
[2024-01-24 13:55:39,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:39,983] [INFO] Task started: CheckM
[2024-01-24 13:55:39,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/checkm_input GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/checkm_result
[2024-01-24 13:56:06,743] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:06,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:06,774] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:06,774] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:06,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/markers.fasta)
[2024-01-24 13:56:06,775] [INFO] Task started: Blastn
[2024-01-24 13:56:06,775] [INFO] Running command: blastn -query GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/markers.fasta -db /var/lib/cwl/stg54a37419-8cf5-48fa-8b24-21f1e37bda89/dqc_reference/reference_markers_gtdb.fasta -out GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:07,920] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:07,925] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:07,925] [INFO] Target genome list was writen to GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:07,945] [INFO] Task started: fastANI
[2024-01-24 13:56:07,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg338bf4b4-a04a-4971-8d7e-d0b1997bd838/GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna.gz --refList GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/target_genomes_gtdb.txt --output GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:15,506] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:15,522] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:15,522] [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_902806985.1	s__Pseudidiomarina piscicola	100.0	831	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000152885.1	s__Idiomarina baltica	80.909	97	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	98.48	98.19	0.90	0.79	8	-
GCF_003987215.1	s__Pseudidiomarina halophila	80.3949	396	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	79.8264	186	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003987045.1	s__Pseudidiomarina marina	79.6119	159	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_001418345.1	s__Pseudidiomarina woesei	79.596	185	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987225.1	s__Pseudidiomarina homiensis	79.5919	316	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987395.1	s__Pseudidiomarina aquimaris	79.5883	313	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	79.3451	183	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_000753735.1	s__Pseudidiomarina atlantica	79.1468	285	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423165.1	s__Pseudidiomarina sediminum	79.0165	251	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987435.1	s__Pseudidiomarina taiwanensis	79.0032	131	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	78.7131	185	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987355.1	s__Pseudidiomarina aestuarii	78.5712	135	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003986955.1	s__Aliidiomarina sedimenti	77.8338	59	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:15,524] [INFO] GTDB search result was written to GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:15,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:15,528] [INFO] DFAST_QC result json was written to GCF_902806985.1_Pseudidiomarina_CECT9734_genomic.fna/dqc_result.json
[2024-01-24 13:56:15,529] [INFO] DFAST_QC completed!
[2024-01-24 13:56:15,529] [INFO] Total running time: 0h0m58s