[2023-03-18 08:17:17,680] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,680] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg123be266-e74c-40fe-afae-472d81dbd488/dqc_reference
[2023-03-18 08:17:18,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,943] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,943] [INFO] Running command: cat /var/lib/cwl/stg655107f0-7ef4-4c04-b82b-74b4ee22c58e/OceanDNA-b41542.fa | prodigal -d OceanDNA-b41542/cds.fna -a OceanDNA-b41542/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:38,325] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:38,325] [INFO] Task started: HMMsearch
[2023-03-18 08:17:38,325] [INFO] Running command: hmmsearch --tblout OceanDNA-b41542/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg123be266-e74c-40fe-afae-472d81dbd488/dqc_reference/reference_markers.hmm OceanDNA-b41542/protein.faa > /dev/null
[2023-03-18 08:17:38,562] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:38,563] [INFO] Found 6/6 markers.
[2023-03-18 08:17:38,584] [INFO] Query marker FASTA was written to OceanDNA-b41542/markers.fasta
[2023-03-18 08:17:38,585] [INFO] Task started: Blastn
[2023-03-18 08:17:38,585] [INFO] Running command: blastn -query OceanDNA-b41542/markers.fasta -db /var/lib/cwl/stg123be266-e74c-40fe-afae-472d81dbd488/dqc_reference/reference_markers.fasta -out OceanDNA-b41542/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:39,222] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:39,223] [INFO] Selected 22 target genomes.
[2023-03-18 08:17:39,224] [INFO] Target genome list was writen to OceanDNA-b41542/target_genomes.txt
[2023-03-18 08:17:39,240] [INFO] Task started: fastANI
[2023-03-18 08:17:39,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg655107f0-7ef4-4c04-b82b-74b4ee22c58e/OceanDNA-b41542.fa --refList OceanDNA-b41542/target_genomes.txt --output OceanDNA-b41542/fastani_result.tsv --threads 1
[2023-03-18 08:17:53,961] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:53,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg123be266-e74c-40fe-afae-472d81dbd488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:53,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg123be266-e74c-40fe-afae-472d81dbd488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:53,967] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:53,967] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:53,967] [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	78.349	266	1113	95	below_threshold
Zhongshania aliphaticivorans	strain=SM-2	GCA_001586255.1	1470434	1470434	type	True	78.3446	270	1113	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	78.2829	266	1113	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	76.8384	99	1113	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	76.3676	100	1113	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:53,967] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41542/tc_result.tsv
[2023-03-18 08:17:53,967] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:53,967] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:53,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg123be266-e74c-40fe-afae-472d81dbd488/dqc_reference/checkm_data
[2023-03-18 08:17:53,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:53,973] [INFO] Task started: CheckM
[2023-03-18 08:17:53,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41542/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41542/checkm_input OceanDNA-b41542/checkm_result
[2023-03-18 08:18:43,119] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:43,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:43,122] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:43,122] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:43,123] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41542/markers.fasta)
[2023-03-18 08:18:43,123] [INFO] Task started: Blastn
[2023-03-18 08:18:43,123] [INFO] Running command: blastn -query OceanDNA-b41542/markers.fasta -db /var/lib/cwl/stg123be266-e74c-40fe-afae-472d81dbd488/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41542/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:44,165] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:44,166] [INFO] Selected 11 target genomes.
[2023-03-18 08:18:44,166] [INFO] Target genome list was writen to OceanDNA-b41542/target_genomes_gtdb.txt
[2023-03-18 08:18:44,176] [INFO] Task started: fastANI
[2023-03-18 08:18:44,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg655107f0-7ef4-4c04-b82b-74b4ee22c58e/OceanDNA-b41542.fa --refList OceanDNA-b41542/target_genomes_gtdb.txt --output OceanDNA-b41542/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:50,888] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:50,895] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:50,895] [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
GCA_018066965.1	s__Marortus sp018066965	80.1191	475	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705855.1	s__Marortus aliphaticivorans_B	80.0524	518	1113	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	79.6806	448	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002915595.1	s__Marortus luteolus	79.6436	461	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	-
GCF_902705875.1	s__Marortus aliphaticivorans_A	78.3901	335	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001586255.1	s__Zhongshania aliphaticivorans	78.3299	271	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	-
GCF_014202945.1	s__Zhongshania antarctica	78.3292	268	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:50,895] [INFO] GTDB search result was written to OceanDNA-b41542/result_gtdb.tsv
[2023-03-18 08:18:50,895] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:50,896] [INFO] DFAST_QC result json was written to OceanDNA-b41542/dqc_result.json
[2023-03-18 08:18:50,896] [INFO] DFAST_QC completed!
[2023-03-18 08:18:50,896] [INFO] Total running time: 0h1m33s