[2024-01-24 14:03:08,143] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,145] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg79ca3a3e-dca6-49ba-9963-d685d9462206/dqc_reference
[2024-01-24 14:03:09,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,642] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c9478f6-e795-4b46-a349-7ce63fdcd1fc/GCF_000355675.1_ASM35567v1_genomic.fna.gz | prodigal -d GCF_000355675.1_ASM35567v1_genomic.fna/cds.fna -a GCF_000355675.1_ASM35567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:19,333] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:19,334] [INFO] Task started: HMMsearch
[2024-01-24 14:03:19,334] [INFO] Running command: hmmsearch --tblout GCF_000355675.1_ASM35567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79ca3a3e-dca6-49ba-9963-d685d9462206/dqc_reference/reference_markers.hmm GCF_000355675.1_ASM35567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:19,672] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:19,674] [INFO] Found 6/6 markers.
[2024-01-24 14:03:19,721] [INFO] Query marker FASTA was written to GCF_000355675.1_ASM35567v1_genomic.fna/markers.fasta
[2024-01-24 14:03:19,721] [INFO] Task started: Blastn
[2024-01-24 14:03:19,722] [INFO] Running command: blastn -query GCF_000355675.1_ASM35567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79ca3a3e-dca6-49ba-9963-d685d9462206/dqc_reference/reference_markers.fasta -out GCF_000355675.1_ASM35567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:20,458] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:20,462] [INFO] Selected 25 target genomes.
[2024-01-24 14:03:20,462] [INFO] Target genome list was writen to GCF_000355675.1_ASM35567v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:20,497] [INFO] Task started: fastANI
[2024-01-24 14:03:20,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c9478f6-e795-4b46-a349-7ce63fdcd1fc/GCF_000355675.1_ASM35567v1_genomic.fna.gz --refList GCF_000355675.1_ASM35567v1_genomic.fna/target_genomes.txt --output GCF_000355675.1_ASM35567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:37,529] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:37,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79ca3a3e-dca6-49ba-9963-d685d9462206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:37,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79ca3a3e-dca6-49ba-9963-d685d9462206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:37,536] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:37,536] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:37,536] [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 oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	100.0	1304	1306	95	conclusive
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	78.6539	190	1306	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	77.722	174	1306	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.3199	110	1306	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	77.1499	111	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:37,538] [INFO] DFAST Taxonomy check result was written to GCF_000355675.1_ASM35567v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:37,539] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:37,539] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:37,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79ca3a3e-dca6-49ba-9963-d685d9462206/dqc_reference/checkm_data
[2024-01-24 14:03:37,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:37,580] [INFO] Task started: CheckM
[2024-01-24 14:03:37,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000355675.1_ASM35567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000355675.1_ASM35567v1_genomic.fna/checkm_input GCF_000355675.1_ASM35567v1_genomic.fna/checkm_result
[2024-01-24 14:04:12,154] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:12,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:12,175] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:12,176] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:12,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000355675.1_ASM35567v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:12,176] [INFO] Task started: Blastn
[2024-01-24 14:04:12,177] [INFO] Running command: blastn -query GCF_000355675.1_ASM35567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79ca3a3e-dca6-49ba-9963-d685d9462206/dqc_reference/reference_markers_gtdb.fasta -out GCF_000355675.1_ASM35567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:13,344] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:13,348] [INFO] Selected 18 target genomes.
[2024-01-24 14:04:13,349] [INFO] Target genome list was writen to GCF_000355675.1_ASM35567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:13,401] [INFO] Task started: fastANI
[2024-01-24 14:04:13,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c9478f6-e795-4b46-a349-7ce63fdcd1fc/GCF_000355675.1_ASM35567v1_genomic.fna.gz --refList GCF_000355675.1_ASM35567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000355675.1_ASM35567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:25,725] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:25,741] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:25,742] [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_000355675.1	s__Thalassolituus oleivorans	100.0	1304	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Thalassolituus	95.0	98.27	98.03	0.89	0.78	10	conclusive
GCA_002733205.1	s__UBA2009 sp002733205	78.6472	209	1306	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_002733645.1	s__Oleibacter sp002733645	78.3464	255	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	97.97	97.97	0.87	0.87	2	-
GCA_014859445.1	s__Bacterioplanes sp014859445	78.1187	135	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000967895.1	s__Oleispira antarctica	77.932	109	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	99.07	99.06	0.98	0.98	3	-
GCA_002298335.1	s__Oleibacter sp002298335	77.9287	124	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	99.94	99.90	0.96	0.95	5	-
GCA_002314145.1	s__UBA2009 sp002314145	77.8934	136	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCF_007785795.1	s__UBA2009 sp002335285	77.8684	221	1306	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_002724925.1	s__Oleibacter sp002724925	77.8664	165	1306	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_002237535.1	s__Bacterioplanes sanyensis_A	77.8387	137	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212115.1	s__Oleibacter sp006212115	76.7913	121	1306	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 14:04:25,744] [INFO] GTDB search result was written to GCF_000355675.1_ASM35567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:25,744] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:25,747] [INFO] DFAST_QC result json was written to GCF_000355675.1_ASM35567v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:25,748] [INFO] DFAST_QC completed!
[2024-01-24 14:04:25,748] [INFO] Total running time: 0h1m18s