[2024-01-24 15:10:48,140] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:48,142] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:48,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg88ebd47b-a169-454c-82d7-6a03d4a56849/dqc_reference
[2024-01-24 15:10:51,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:51,751] [INFO] Task started: Prodigal
[2024-01-24 15:10:51,751] [INFO] Running command: gunzip -c /var/lib/cwl/stgb28fc8fb-6bfb-471f-bc64-ac9a77cd7248/GCF_003855155.1_ASM385515v1_genomic.fna.gz | prodigal -d GCF_003855155.1_ASM385515v1_genomic.fna/cds.fna -a GCF_003855155.1_ASM385515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:03,543] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:03,543] [INFO] Task started: HMMsearch
[2024-01-24 15:11:03,543] [INFO] Running command: hmmsearch --tblout GCF_003855155.1_ASM385515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88ebd47b-a169-454c-82d7-6a03d4a56849/dqc_reference/reference_markers.hmm GCF_003855155.1_ASM385515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:03,866] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:03,868] [INFO] Found 6/6 markers.
[2024-01-24 15:11:03,913] [INFO] Query marker FASTA was written to GCF_003855155.1_ASM385515v1_genomic.fna/markers.fasta
[2024-01-24 15:11:03,914] [INFO] Task started: Blastn
[2024-01-24 15:11:03,914] [INFO] Running command: blastn -query GCF_003855155.1_ASM385515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88ebd47b-a169-454c-82d7-6a03d4a56849/dqc_reference/reference_markers.fasta -out GCF_003855155.1_ASM385515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:04,678] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:04,681] [INFO] Selected 8 target genomes.
[2024-01-24 15:11:04,682] [INFO] Target genome list was writen to GCF_003855155.1_ASM385515v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:04,686] [INFO] Task started: fastANI
[2024-01-24 15:11:04,686] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28fc8fb-6bfb-471f-bc64-ac9a77cd7248/GCF_003855155.1_ASM385515v1_genomic.fna.gz --refList GCF_003855155.1_ASM385515v1_genomic.fna/target_genomes.txt --output GCF_003855155.1_ASM385515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:15,335] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:15,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88ebd47b-a169-454c-82d7-6a03d4a56849/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:15,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88ebd47b-a169-454c-82d7-6a03d4a56849/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:15,349] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:15,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:15,349] [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 psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	100.0	1710	1711	95	conclusive
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	99.9103	1575	1711	95	conclusive
Shewanella livingstonensis	strain=LMG 19866	GCA_003855395.1	150120	150120	type	True	85.4625	1226	1711	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	84.5429	1169	1711	95	below_threshold
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	84.4651	1184	1711	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	83.9809	1151	1711	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	80.891	848	1711	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	80.6146	807	1711	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:15,351] [INFO] DFAST Taxonomy check result was written to GCF_003855155.1_ASM385515v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:15,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:15,352] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:15,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88ebd47b-a169-454c-82d7-6a03d4a56849/dqc_reference/checkm_data
[2024-01-24 15:11:15,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:15,402] [INFO] Task started: CheckM
[2024-01-24 15:11:15,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003855155.1_ASM385515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003855155.1_ASM385515v1_genomic.fna/checkm_input GCF_003855155.1_ASM385515v1_genomic.fna/checkm_result
[2024-01-24 15:11:54,754] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:54,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:54,783] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:54,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:54,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003855155.1_ASM385515v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:54,785] [INFO] Task started: Blastn
[2024-01-24 15:11:54,785] [INFO] Running command: blastn -query GCF_003855155.1_ASM385515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88ebd47b-a169-454c-82d7-6a03d4a56849/dqc_reference/reference_markers_gtdb.fasta -out GCF_003855155.1_ASM385515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:55,988] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:55,992] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:55,992] [INFO] Target genome list was writen to GCF_003855155.1_ASM385515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:55,998] [INFO] Task started: fastANI
[2024-01-24 15:11:55,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28fc8fb-6bfb-471f-bc64-ac9a77cd7248/GCF_003855155.1_ASM385515v1_genomic.fna.gz --refList GCF_003855155.1_ASM385515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003855155.1_ASM385515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:05,823] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:05,833] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:05,833] [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_003855155.1	s__Shewanella sp002836275	100.0	1710	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	conclusive
GCF_010092445.1	s__Shewanella sp002836315	86.0658	1240	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_003797125.1	s__Shewanella frigidimarina	85.7775	1222	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_003855395.1	s__Shewanella livingstonensis	85.4598	1228	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014164505.1	s__Shewanella sp014164505	85.4255	969	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797885.1	s__Shewanella vesiculosa	84.465	1185	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	-
GCF_006385555.1	s__Shewanella polaris	83.95	1151	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:05,835] [INFO] GTDB search result was written to GCF_003855155.1_ASM385515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:05,836] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:05,840] [INFO] DFAST_QC result json was written to GCF_003855155.1_ASM385515v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:05,841] [INFO] DFAST_QC completed!
[2024-01-24 15:12:05,841] [INFO] Total running time: 0h1m18s