[2024-01-24 11:44:05,458] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg56f1d0db-c227-4337-b639-994dcab3de6c/dqc_reference
[2024-01-24 11:44:08,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,837] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,837] [INFO] Running command: gunzip -c /var/lib/cwl/stgd11eb6b3-6760-43c7-9e95-4fd10f926e08/GCF_001586255.1_ASM158625v1_genomic.fna.gz | prodigal -d GCF_001586255.1_ASM158625v1_genomic.fna/cds.fna -a GCF_001586255.1_ASM158625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:19,820] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:19,820] [INFO] Task started: HMMsearch
[2024-01-24 11:44:19,821] [INFO] Running command: hmmsearch --tblout GCF_001586255.1_ASM158625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56f1d0db-c227-4337-b639-994dcab3de6c/dqc_reference/reference_markers.hmm GCF_001586255.1_ASM158625v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:20,075] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:20,076] [INFO] Found 6/6 markers.
[2024-01-24 11:44:20,113] [INFO] Query marker FASTA was written to GCF_001586255.1_ASM158625v1_genomic.fna/markers.fasta
[2024-01-24 11:44:20,113] [INFO] Task started: Blastn
[2024-01-24 11:44:20,114] [INFO] Running command: blastn -query GCF_001586255.1_ASM158625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56f1d0db-c227-4337-b639-994dcab3de6c/dqc_reference/reference_markers.fasta -out GCF_001586255.1_ASM158625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:20,803] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:20,807] [INFO] Selected 17 target genomes.
[2024-01-24 11:44:20,807] [INFO] Target genome list was writen to GCF_001586255.1_ASM158625v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:20,815] [INFO] Task started: fastANI
[2024-01-24 11:44:20,815] [INFO] Running command: fastANI --query /var/lib/cwl/stgd11eb6b3-6760-43c7-9e95-4fd10f926e08/GCF_001586255.1_ASM158625v1_genomic.fna.gz --refList GCF_001586255.1_ASM158625v1_genomic.fna/target_genomes.txt --output GCF_001586255.1_ASM158625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:32,784] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:32,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56f1d0db-c227-4337-b639-994dcab3de6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:32,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56f1d0db-c227-4337-b639-994dcab3de6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:32,792] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:32,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:32,793] [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
Zhongshania aliphaticivorans	strain=SM-2	GCA_001586255.1	1470434	1470434	type	True	100.0	1400	1401	95	conclusive
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	92.4279	1064	1401	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	92.3744	1076	1401	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	78.2462	213	1401	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	77.5218	148	1401	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.4631	171	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:32,795] [INFO] DFAST Taxonomy check result was written to GCF_001586255.1_ASM158625v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:32,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:32,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:32,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56f1d0db-c227-4337-b639-994dcab3de6c/dqc_reference/checkm_data
[2024-01-24 11:44:32,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:32,839] [INFO] Task started: CheckM
[2024-01-24 11:44:32,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001586255.1_ASM158625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001586255.1_ASM158625v1_genomic.fna/checkm_input GCF_001586255.1_ASM158625v1_genomic.fna/checkm_result
[2024-01-24 11:45:08,354] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:08,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:08,372] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:08,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:08,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001586255.1_ASM158625v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:08,373] [INFO] Task started: Blastn
[2024-01-24 11:45:08,373] [INFO] Running command: blastn -query GCF_001586255.1_ASM158625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56f1d0db-c227-4337-b639-994dcab3de6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001586255.1_ASM158625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:09,548] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:09,553] [INFO] Selected 17 target genomes.
[2024-01-24 11:45:09,553] [INFO] Target genome list was writen to GCF_001586255.1_ASM158625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:09,582] [INFO] Task started: fastANI
[2024-01-24 11:45:09,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgd11eb6b3-6760-43c7-9e95-4fd10f926e08/GCF_001586255.1_ASM158625v1_genomic.fna.gz --refList GCF_001586255.1_ASM158625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001586255.1_ASM158625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:22,145] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:22,157] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:22,158] [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_001586255.1	s__Zhongshania aliphaticivorans	100.0	1399	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	conclusive
GCF_014202945.1	s__Zhongshania antarctica	92.4279	1064	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902705875.1	s__Marortus aliphaticivorans_A	79.7671	276	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002915595.1	s__Marortus luteolus	79.4719	399	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	-
GCF_902705855.1	s__Marortus aliphaticivorans_B	79.4691	397	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067195.1	s__Marortus sp018067195	78.7191	320	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066965.1	s__Marortus sp018066965	78.6796	355	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010805.1	s__IMCC21906 sp001010805	78.5159	182	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272835.1	s__Spongiibacter sp012272835	78.2462	213	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705705.1	s__KMU-158 sp014705705	77.4467	172	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:22,159] [INFO] GTDB search result was written to GCF_001586255.1_ASM158625v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:22,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:22,162] [INFO] DFAST_QC result json was written to GCF_001586255.1_ASM158625v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:22,163] [INFO] DFAST_QC completed!
[2024-01-24 11:45:22,163] [INFO] Total running time: 0h1m17s