[2024-01-24 15:26:35,781] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:35,784] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:35,784] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5a9982e-ceb2-49fa-82c3-cfa098d07d6a/dqc_reference
[2024-01-24 15:26:39,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,061] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b0f13ee-bcc5-45d5-8f8f-3417ae553644/GCF_014652515.1_ASM1465251v1_genomic.fna.gz | prodigal -d GCF_014652515.1_ASM1465251v1_genomic.fna/cds.fna -a GCF_014652515.1_ASM1465251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:50,604] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:50,604] [INFO] Task started: HMMsearch
[2024-01-24 15:26:50,604] [INFO] Running command: hmmsearch --tblout GCF_014652515.1_ASM1465251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5a9982e-ceb2-49fa-82c3-cfa098d07d6a/dqc_reference/reference_markers.hmm GCF_014652515.1_ASM1465251v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:50,895] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:50,896] [INFO] Found 6/6 markers.
[2024-01-24 15:26:50,931] [INFO] Query marker FASTA was written to GCF_014652515.1_ASM1465251v1_genomic.fna/markers.fasta
[2024-01-24 15:26:50,931] [INFO] Task started: Blastn
[2024-01-24 15:26:50,931] [INFO] Running command: blastn -query GCF_014652515.1_ASM1465251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5a9982e-ceb2-49fa-82c3-cfa098d07d6a/dqc_reference/reference_markers.fasta -out GCF_014652515.1_ASM1465251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:51,768] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:51,772] [INFO] Selected 22 target genomes.
[2024-01-24 15:26:51,773] [INFO] Target genome list was writen to GCF_014652515.1_ASM1465251v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:51,781] [INFO] Task started: fastANI
[2024-01-24 15:26:51,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b0f13ee-bcc5-45d5-8f8f-3417ae553644/GCF_014652515.1_ASM1465251v1_genomic.fna.gz --refList GCF_014652515.1_ASM1465251v1_genomic.fna/target_genomes.txt --output GCF_014652515.1_ASM1465251v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:08,605] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:08,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5a9982e-ceb2-49fa-82c3-cfa098d07d6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:08,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5a9982e-ceb2-49fa-82c3-cfa098d07d6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:08,616] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:08,617] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:08,617] [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
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	100.0	1259	1260	95	conclusive
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	77.7784	122	1260	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	77.5003	183	1260	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.4324	149	1260	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	77.3577	165	1260	95	below_threshold
Bermanella marisrubri	strain=RED65	GCA_012295615.1	207949	207949	type	True	76.375	50	1260	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	76.0328	54	1260	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	75.7374	53	1260	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.4607	52	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:08,618] [INFO] DFAST Taxonomy check result was written to GCF_014652515.1_ASM1465251v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:08,619] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:08,619] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:08,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5a9982e-ceb2-49fa-82c3-cfa098d07d6a/dqc_reference/checkm_data
[2024-01-24 15:27:08,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:08,662] [INFO] Task started: CheckM
[2024-01-24 15:27:08,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652515.1_ASM1465251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652515.1_ASM1465251v1_genomic.fna/checkm_input GCF_014652515.1_ASM1465251v1_genomic.fna/checkm_result
[2024-01-24 15:27:46,727] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:46,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:46,748] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:46,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:46,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652515.1_ASM1465251v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:46,749] [INFO] Task started: Blastn
[2024-01-24 15:27:46,749] [INFO] Running command: blastn -query GCF_014652515.1_ASM1465251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5a9982e-ceb2-49fa-82c3-cfa098d07d6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652515.1_ASM1465251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:48,073] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:48,079] [INFO] Selected 22 target genomes.
[2024-01-24 15:27:48,080] [INFO] Target genome list was writen to GCF_014652515.1_ASM1465251v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:48,098] [INFO] Task started: fastANI
[2024-01-24 15:27:48,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b0f13ee-bcc5-45d5-8f8f-3417ae553644/GCF_014652515.1_ASM1465251v1_genomic.fna.gz --refList GCF_014652515.1_ASM1465251v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652515.1_ASM1465251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:03,171] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:03,191] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:03,191] [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_014652515.1	s__Bacterioplanes sanyensis	100.0	1259	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002237535.1	s__Bacterioplanes sanyensis_A	81.4582	722	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156675.1	s__Oleibacter marinus	77.7996	121	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCA_002724925.1	s__Oleibacter sp002724925	77.7985	131	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.64	97.85	0.94	0.89	5	-
GCA_002733205.1	s__UBA2009 sp002733205	77.7759	215	1260	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_002314145.1	s__UBA2009 sp002314145	77.768	169	1260	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_016132445.1	s__UBA2009 sp016132445	77.6458	211	1260	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	77.6337	158	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCF_007785795.1	s__UBA2009 sp002335285	77.5344	251	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_002331105.1	s__Oleibacter sp002331105	77.4337	108	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	97.07	0.90	0.84	7	-
GCF_000422845.1	s__Oceanobacter kriegii	77.3738	164	1260	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	76.6797	91	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012295615.1	s__Bermanella marisrubri	76.3852	50	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	99.98	99.98	0.99	0.99	2	-
GCA_013373125.1	s__Bermanella sp013373125	75.8468	57	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	75.5006	50	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:03,193] [INFO] GTDB search result was written to GCF_014652515.1_ASM1465251v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:03,193] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:03,197] [INFO] DFAST_QC result json was written to GCF_014652515.1_ASM1465251v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:03,197] [INFO] DFAST_QC completed!
[2024-01-24 15:28:03,197] [INFO] Total running time: 0h1m27s