[2024-01-24 14:14:31,881] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:31,884] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:31,884] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ea58fa4-3220-4d9b-a4ad-e644fed1de3b/dqc_reference
[2024-01-24 14:14:33,121] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:33,122] [INFO] Task started: Prodigal
[2024-01-24 14:14:33,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg291e9643-08f3-4f0e-a2de-cf1385d62782/GCF_014202945.1_ASM1420294v1_genomic.fna.gz | prodigal -d GCF_014202945.1_ASM1420294v1_genomic.fna/cds.fna -a GCF_014202945.1_ASM1420294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:43,032] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:43,033] [INFO] Task started: HMMsearch
[2024-01-24 14:14:43,033] [INFO] Running command: hmmsearch --tblout GCF_014202945.1_ASM1420294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ea58fa4-3220-4d9b-a4ad-e644fed1de3b/dqc_reference/reference_markers.hmm GCF_014202945.1_ASM1420294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:43,346] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:43,347] [INFO] Found 6/6 markers.
[2024-01-24 14:14:43,386] [INFO] Query marker FASTA was written to GCF_014202945.1_ASM1420294v1_genomic.fna/markers.fasta
[2024-01-24 14:14:43,386] [INFO] Task started: Blastn
[2024-01-24 14:14:43,386] [INFO] Running command: blastn -query GCF_014202945.1_ASM1420294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ea58fa4-3220-4d9b-a4ad-e644fed1de3b/dqc_reference/reference_markers.fasta -out GCF_014202945.1_ASM1420294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:44,092] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:44,096] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:44,096] [INFO] Target genome list was writen to GCF_014202945.1_ASM1420294v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:44,134] [INFO] Task started: fastANI
[2024-01-24 14:14:44,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg291e9643-08f3-4f0e-a2de-cf1385d62782/GCF_014202945.1_ASM1420294v1_genomic.fna.gz --refList GCF_014202945.1_ASM1420294v1_genomic.fna/target_genomes.txt --output GCF_014202945.1_ASM1420294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:55,666] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:55,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ea58fa4-3220-4d9b-a4ad-e644fed1de3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:55,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ea58fa4-3220-4d9b-a4ad-e644fed1de3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:55,673] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:55,674] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:55,674] [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 antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	100.0	1268	1273	95	conclusive
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	99.9834	1254	1273	95	conclusive
Zhongshania aliphaticivorans	strain=SM-2	GCA_001586255.1	1470434	1470434	type	True	92.4819	1072	1273	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.5056	147	1273	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	77.4326	194	1273	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	77.3422	157	1273	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	76.9923	173	1273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:55,675] [INFO] DFAST Taxonomy check result was written to GCF_014202945.1_ASM1420294v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:55,676] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:55,676] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:55,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ea58fa4-3220-4d9b-a4ad-e644fed1de3b/dqc_reference/checkm_data
[2024-01-24 14:14:55,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:55,718] [INFO] Task started: CheckM
[2024-01-24 14:14:55,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202945.1_ASM1420294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202945.1_ASM1420294v1_genomic.fna/checkm_input GCF_014202945.1_ASM1420294v1_genomic.fna/checkm_result
[2024-01-24 14:15:29,647] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:29,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:29,668] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:29,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:29,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202945.1_ASM1420294v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:29,670] [INFO] Task started: Blastn
[2024-01-24 14:15:29,670] [INFO] Running command: blastn -query GCF_014202945.1_ASM1420294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ea58fa4-3220-4d9b-a4ad-e644fed1de3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202945.1_ASM1420294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:30,869] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:30,874] [INFO] Selected 15 target genomes.
[2024-01-24 14:15:30,874] [INFO] Target genome list was writen to GCF_014202945.1_ASM1420294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:30,904] [INFO] Task started: fastANI
[2024-01-24 14:15:30,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg291e9643-08f3-4f0e-a2de-cf1385d62782/GCF_014202945.1_ASM1420294v1_genomic.fna.gz --refList GCF_014202945.1_ASM1420294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202945.1_ASM1420294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:41,302] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:41,313] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:41,314] [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_014202945.1	s__Zhongshania antarctica	100.0	1268	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001586255.1	s__Zhongshania aliphaticivorans	92.4856	1071	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	-
GCF_902705855.1	s__Marortus aliphaticivorans_B	79.795	361	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705875.1	s__Marortus aliphaticivorans_A	79.2134	254	1273	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	79.0379	360	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	-
GCA_018067195.1	s__Marortus sp018067195	78.5012	317	1273	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	77.5261	183	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422345.1	s__Spongiibacter marinus_A	77.4756	153	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272835.1	s__Spongiibacter sp012272835	77.4326	194	1273	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	76.9916	174	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900120175.1	s__Oceanicoccus sp900120175	76.5866	52	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-21967;g__Oceanicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:41,316] [INFO] GTDB search result was written to GCF_014202945.1_ASM1420294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:41,317] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:41,322] [INFO] DFAST_QC result json was written to GCF_014202945.1_ASM1420294v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:41,323] [INFO] DFAST_QC completed!
[2024-01-24 14:15:41,323] [INFO] Total running time: 0h1m9s