[2024-01-24 13:22:27,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:27,040] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:27,040] [INFO] DQC Reference Directory: /var/lib/cwl/stgff42803f-fe6b-4809-9b35-40379c78c914/dqc_reference
[2024-01-24 13:22:28,353] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:28,354] [INFO] Task started: Prodigal
[2024-01-24 13:22:28,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg41388c96-98f6-49e7-829f-7db78011ec49/GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/cds.fna -a GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:38,597] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:38,598] [INFO] Task started: HMMsearch
[2024-01-24 13:22:38,598] [INFO] Running command: hmmsearch --tblout GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff42803f-fe6b-4809-9b35-40379c78c914/dqc_reference/reference_markers.hmm GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:38,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:38,942] [INFO] Found 6/6 markers.
[2024-01-24 13:22:38,993] [INFO] Query marker FASTA was written to GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:38,994] [INFO] Task started: Blastn
[2024-01-24 13:22:38,994] [INFO] Running command: blastn -query GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgff42803f-fe6b-4809-9b35-40379c78c914/dqc_reference/reference_markers.fasta -out GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:40,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:40,117] [INFO] Selected 11 target genomes.
[2024-01-24 13:22:40,117] [INFO] Target genome list was writen to GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:40,133] [INFO] Task started: fastANI
[2024-01-24 13:22:40,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg41388c96-98f6-49e7-829f-7db78011ec49/GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna.gz --refList GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:50,183] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:50,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff42803f-fe6b-4809-9b35-40379c78c914/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:50,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff42803f-fe6b-4809-9b35-40379c78c914/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:50,207] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:50,207] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:50,207] [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
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	100.0	1481	1486	95	conclusive
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	99.987	1479	1486	95	conclusive
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	83.946	1044	1486	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	83.9186	1056	1486	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	83.8484	1055	1486	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	83.3339	980	1486	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	79.5958	91	1486	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	76.5077	61	1486	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.3112	67	1486	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	76.1584	66	1486	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	75.724	73	1486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:50,215] [INFO] DFAST Taxonomy check result was written to GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:50,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:50,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:50,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff42803f-fe6b-4809-9b35-40379c78c914/dqc_reference/checkm_data
[2024-01-24 13:22:50,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:50,277] [INFO] Task started: CheckM
[2024-01-24 13:22:50,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/checkm_input GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:24,532] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:24,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:24,561] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:24,562] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:24,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:24,563] [INFO] Task started: Blastn
[2024-01-24 13:23:24,563] [INFO] Running command: blastn -query GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgff42803f-fe6b-4809-9b35-40379c78c914/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:25,793] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:25,797] [INFO] Selected 11 target genomes.
[2024-01-24 13:23:25,797] [INFO] Target genome list was writen to GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:25,811] [INFO] Task started: fastANI
[2024-01-24 13:23:25,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg41388c96-98f6-49e7-829f-7db78011ec49/GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna.gz --refList GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:36,772] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:36,790] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:36,791] [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_900116435.1	s__Pseudoalteromonas lipolytica	100.0	1481	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	conclusive
GCA_002684115.1	s__Pseudoalteromonas sp002684115	85.749	225	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	97.90	97.71	0.79	0.79	5	-
GCF_013391845.1	s__Pseudoalteromonas sp002685175	84.0455	861	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	83.9183	1056	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	83.8484	1055	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	83.8218	1008	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	83.7564	1015	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_013349995.1	s__Pseudoalteromonas sp013349995	83.7561	1010	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.6093	97.46	97.37	0.85	0.84	6	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	83.7028	1039	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	83.5691	1006	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_001550155.1	s__Pseudoalteromonas arabiensis	83.3339	980	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:36,793] [INFO] GTDB search result was written to GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:36,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:36,797] [INFO] DFAST_QC result json was written to GCF_900116435.1_IMG-taxon_2617270886_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:36,798] [INFO] DFAST_QC completed!
[2024-01-24 13:23:36,798] [INFO] Total running time: 0h1m10s