[2024-01-24 13:09:27,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:27,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:27,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a20ceed-279a-4f9d-9cae-fa68e0541109/dqc_reference
[2024-01-24 13:09:28,733] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:28,734] [INFO] Task started: Prodigal
[2024-01-24 13:09:28,734] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e042a28-f266-4af3-a67f-1b20e008a2f2/GCF_030161835.1_ASM3016183v1_genomic.fna.gz | prodigal -d GCF_030161835.1_ASM3016183v1_genomic.fna/cds.fna -a GCF_030161835.1_ASM3016183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:39,331] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:39,332] [INFO] Task started: HMMsearch
[2024-01-24 13:09:39,332] [INFO] Running command: hmmsearch --tblout GCF_030161835.1_ASM3016183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a20ceed-279a-4f9d-9cae-fa68e0541109/dqc_reference/reference_markers.hmm GCF_030161835.1_ASM3016183v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:39,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:39,601] [INFO] Found 6/6 markers.
[2024-01-24 13:09:39,651] [INFO] Query marker FASTA was written to GCF_030161835.1_ASM3016183v1_genomic.fna/markers.fasta
[2024-01-24 13:09:39,652] [INFO] Task started: Blastn
[2024-01-24 13:09:39,652] [INFO] Running command: blastn -query GCF_030161835.1_ASM3016183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a20ceed-279a-4f9d-9cae-fa68e0541109/dqc_reference/reference_markers.fasta -out GCF_030161835.1_ASM3016183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:40,405] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:40,408] [INFO] Selected 10 target genomes.
[2024-01-24 13:09:40,408] [INFO] Target genome list was writen to GCF_030161835.1_ASM3016183v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:40,413] [INFO] Task started: fastANI
[2024-01-24 13:09:40,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e042a28-f266-4af3-a67f-1b20e008a2f2/GCF_030161835.1_ASM3016183v1_genomic.fna.gz --refList GCF_030161835.1_ASM3016183v1_genomic.fna/target_genomes.txt --output GCF_030161835.1_ASM3016183v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:51,739] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:51,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a20ceed-279a-4f9d-9cae-fa68e0541109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:51,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a20ceed-279a-4f9d-9cae-fa68e0541109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:51,748] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:09:51,749] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:51,749] [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
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	99.9522	1343	1535	95	conclusive
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	99.7914	1159	1535	95	conclusive
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	93.6106	1206	1535	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	85.8139	1159	1535	95	below_threshold
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	85.2095	1078	1535	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	85.1832	1097	1535	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	82.9008	912	1535	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	80.4259	795	1535	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	80.2948	800	1535	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	78.6572	280	1535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:51,751] [INFO] DFAST Taxonomy check result was written to GCF_030161835.1_ASM3016183v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:51,752] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:51,752] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:51,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a20ceed-279a-4f9d-9cae-fa68e0541109/dqc_reference/checkm_data
[2024-01-24 13:09:51,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:51,804] [INFO] Task started: CheckM
[2024-01-24 13:09:51,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161835.1_ASM3016183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161835.1_ASM3016183v1_genomic.fna/checkm_input GCF_030161835.1_ASM3016183v1_genomic.fna/checkm_result
[2024-01-24 13:10:27,392] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:27,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:27,416] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:27,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:27,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161835.1_ASM3016183v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:27,417] [INFO] Task started: Blastn
[2024-01-24 13:10:27,417] [INFO] Running command: blastn -query GCF_030161835.1_ASM3016183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a20ceed-279a-4f9d-9cae-fa68e0541109/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161835.1_ASM3016183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:28,501] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:28,505] [INFO] Selected 8 target genomes.
[2024-01-24 13:10:28,505] [INFO] Target genome list was writen to GCF_030161835.1_ASM3016183v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:28,512] [INFO] Task started: fastANI
[2024-01-24 13:10:28,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e042a28-f266-4af3-a67f-1b20e008a2f2/GCF_030161835.1_ASM3016183v1_genomic.fna.gz --refList GCF_030161835.1_ASM3016183v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161835.1_ASM3016183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:38,511] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:38,524] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:10:38,524] [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_900156405.1	s__Shewanella morhuae	93.6136	1206	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_900456975.1	s__Shewanella baltica	85.8452	1163	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_002838165.1	s__Shewanella sp002838165	85.4083	1126	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_002966515.1	s__Shewanella sp002966515	85.3798	1138	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCF_016406325.1	s__Shewanella putrefaciens	82.8131	943	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCA_002783505.1	s__Shewanella sp002783505	82.6091	871	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406305.1	s__Shewanella putrefaciens_C	82.5838	938	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203935.1	s__Shewanella sp000203935	80.5883	817	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:38,526] [INFO] GTDB search result was written to GCF_030161835.1_ASM3016183v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:38,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:38,531] [INFO] DFAST_QC result json was written to GCF_030161835.1_ASM3016183v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:38,531] [INFO] DFAST_QC completed!
[2024-01-24 13:10:38,531] [INFO] Total running time: 0h1m11s