[2024-01-24 13:48:59,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg96844dae-41b6-4dcd-952b-25be621e4708/dqc_reference
[2024-01-24 13:49:00,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,907] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,908] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9c49746-56bc-44c7-896f-dd99d4d6111d/GCF_020447205.1_ASM2044720v1_genomic.fna.gz | prodigal -d GCF_020447205.1_ASM2044720v1_genomic.fna/cds.fna -a GCF_020447205.1_ASM2044720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:12,309] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:12,309] [INFO] Task started: HMMsearch
[2024-01-24 13:49:12,310] [INFO] Running command: hmmsearch --tblout GCF_020447205.1_ASM2044720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96844dae-41b6-4dcd-952b-25be621e4708/dqc_reference/reference_markers.hmm GCF_020447205.1_ASM2044720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:12,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:12,581] [INFO] Found 6/6 markers.
[2024-01-24 13:49:12,621] [INFO] Query marker FASTA was written to GCF_020447205.1_ASM2044720v1_genomic.fna/markers.fasta
[2024-01-24 13:49:12,622] [INFO] Task started: Blastn
[2024-01-24 13:49:12,622] [INFO] Running command: blastn -query GCF_020447205.1_ASM2044720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96844dae-41b6-4dcd-952b-25be621e4708/dqc_reference/reference_markers.fasta -out GCF_020447205.1_ASM2044720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:13,409] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:13,412] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:13,413] [INFO] Target genome list was writen to GCF_020447205.1_ASM2044720v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:13,418] [INFO] Task started: fastANI
[2024-01-24 13:49:13,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9c49746-56bc-44c7-896f-dd99d4d6111d/GCF_020447205.1_ASM2044720v1_genomic.fna.gz --refList GCF_020447205.1_ASM2044720v1_genomic.fna/target_genomes.txt --output GCF_020447205.1_ASM2044720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:25,416] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:25,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96844dae-41b6-4dcd-952b-25be621e4708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:25,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96844dae-41b6-4dcd-952b-25be621e4708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:25,430] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:25,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:25,431] [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
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	80.0148	559	1439	95	below_threshold
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	79.0716	243	1439	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	78.6977	229	1439	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	78.2739	270	1439	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	78.2256	288	1439	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.153	249	1439	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	76.5941	87	1439	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.4852	87	1439	95	below_threshold
Atopomonas hussainii	strain=JCM 19513	GCA_900109735.1	1429083	1429083	type	True	76.3902	106	1439	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	76.3097	69	1439	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.2601	61	1439	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	76.2314	81	1439	95	below_threshold
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	76.1084	66	1439	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.0304	71	1439	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.9853	69	1439	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.9742	71	1439	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	75.8928	65	1439	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	75.7244	71	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:25,434] [INFO] DFAST Taxonomy check result was written to GCF_020447205.1_ASM2044720v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:25,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:25,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:25,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96844dae-41b6-4dcd-952b-25be621e4708/dqc_reference/checkm_data
[2024-01-24 13:49:25,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:25,481] [INFO] Task started: CheckM
[2024-01-24 13:49:25,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020447205.1_ASM2044720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020447205.1_ASM2044720v1_genomic.fna/checkm_input GCF_020447205.1_ASM2044720v1_genomic.fna/checkm_result
[2024-01-24 13:50:04,100] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:04,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,130] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:04,130] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:04,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020447205.1_ASM2044720v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:04,131] [INFO] Task started: Blastn
[2024-01-24 13:50:04,131] [INFO] Running command: blastn -query GCF_020447205.1_ASM2044720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96844dae-41b6-4dcd-952b-25be621e4708/dqc_reference/reference_markers_gtdb.fasta -out GCF_020447205.1_ASM2044720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:05,505] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:05,508] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:05,508] [INFO] Target genome list was writen to GCF_020447205.1_ASM2044720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:05,514] [INFO] Task started: fastANI
[2024-01-24 13:50:05,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9c49746-56bc-44c7-896f-dd99d4d6111d/GCF_020447205.1_ASM2044720v1_genomic.fna.gz --refList GCF_020447205.1_ASM2044720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020447205.1_ASM2044720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:13,067] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:13,076] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:13,076] [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_007785795.1	s__UBA2009 sp002335285	97.6945	1329	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	conclusive
GCA_002733205.1	s__UBA2009 sp002733205	88.8159	1058	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	96.83	96.83	0.84	0.84	2	-
GCA_016132445.1	s__UBA2009 sp016132445	80.4218	573	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCA_002706025.1	s__UBA2009 sp002706025	79.3552	481	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCA_002314145.1	s__UBA2009 sp002314145	78.8067	493	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCA_002724925.1	s__Oleibacter sp002724925	78.2771	233	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.64	97.85	0.94	0.89	5	-
GCF_000422845.1	s__Oceanobacter kriegii	78.2042	289	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212115.1	s__Oleibacter sp006212115	77.474	158	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:13,078] [INFO] GTDB search result was written to GCF_020447205.1_ASM2044720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:13,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:13,082] [INFO] DFAST_QC result json was written to GCF_020447205.1_ASM2044720v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:13,083] [INFO] DFAST_QC completed!
[2024-01-24 13:50:13,083] [INFO] Total running time: 0h1m13s