[2023-03-16 03:47:32,863] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,863] [INFO] DQC Reference Directory: /var/lib/cwl/stge5837ba3-70b1-4683-9401-3219fc580a7f/dqc_reference
[2023-03-16 03:47:34,484] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,484] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,485] [INFO] Running command: cat /var/lib/cwl/stg37ea2495-228d-42ee-9b89-f591422cd205/OceanDNA-b16160.fa | prodigal -d OceanDNA-b16160/cds.fna -a OceanDNA-b16160/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:56,903] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:56,904] [INFO] Task started: HMMsearch
[2023-03-16 03:47:56,904] [INFO] Running command: hmmsearch --tblout OceanDNA-b16160/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5837ba3-70b1-4683-9401-3219fc580a7f/dqc_reference/reference_markers.hmm OceanDNA-b16160/protein.faa > /dev/null
[2023-03-16 03:47:57,148] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:57,149] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg37ea2495-228d-42ee-9b89-f591422cd205/OceanDNA-b16160.fa]
[2023-03-16 03:47:57,175] [INFO] Query marker FASTA was written to OceanDNA-b16160/markers.fasta
[2023-03-16 03:47:57,176] [INFO] Task started: Blastn
[2023-03-16 03:47:57,176] [INFO] Running command: blastn -query OceanDNA-b16160/markers.fasta -db /var/lib/cwl/stge5837ba3-70b1-4683-9401-3219fc580a7f/dqc_reference/reference_markers.fasta -out OceanDNA-b16160/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:57,698] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:57,699] [INFO] Selected 15 target genomes.
[2023-03-16 03:47:57,699] [INFO] Target genome list was writen to OceanDNA-b16160/target_genomes.txt
[2023-03-16 03:47:57,709] [INFO] Task started: fastANI
[2023-03-16 03:47:57,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ea2495-228d-42ee-9b89-f591422cd205/OceanDNA-b16160.fa --refList OceanDNA-b16160/target_genomes.txt --output OceanDNA-b16160/fastani_result.tsv --threads 1
[2023-03-16 03:48:10,593] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:10,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5837ba3-70b1-4683-9401-3219fc580a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:10,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5837ba3-70b1-4683-9401-3219fc580a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:10,597] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:10,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:10,597] [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
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	76.1552	183	1227	95	below_threshold
Waterburya agarophytonicola	strain=KI4	GCA_020640915.1	2886916	2886916	type	True	76.0797	162	1227	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:10,597] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16160/tc_result.tsv
[2023-03-16 03:48:10,598] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:10,598] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:10,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5837ba3-70b1-4683-9401-3219fc580a7f/dqc_reference/checkm_data
[2023-03-16 03:48:10,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:10,604] [INFO] Task started: CheckM
[2023-03-16 03:48:10,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16160/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16160/checkm_input OceanDNA-b16160/checkm_result
[2023-03-16 03:49:06,632] [INFO] Task succeeded: CheckM
[2023-03-16 03:49:06,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:49:06,635] [INFO] ===== Completeness check finished =====
[2023-03-16 03:49:06,635] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:49:06,636] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16160/markers.fasta)
[2023-03-16 03:49:06,636] [INFO] Task started: Blastn
[2023-03-16 03:49:06,636] [INFO] Running command: blastn -query OceanDNA-b16160/markers.fasta -db /var/lib/cwl/stge5837ba3-70b1-4683-9401-3219fc580a7f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16160/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:49:07,392] [INFO] Task succeeded: Blastn
[2023-03-16 03:49:07,393] [INFO] Selected 17 target genomes.
[2023-03-16 03:49:07,393] [INFO] Target genome list was writen to OceanDNA-b16160/target_genomes_gtdb.txt
[2023-03-16 03:49:07,516] [INFO] Task started: fastANI
[2023-03-16 03:49:07,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ea2495-228d-42ee-9b89-f591422cd205/OceanDNA-b16160.fa --refList OceanDNA-b16160/target_genomes_gtdb.txt --output OceanDNA-b16160/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:49:23,422] [INFO] Task succeeded: fastANI
[2023-03-16 03:49:23,429] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:49:23,429] [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_900659865.1	s__Hyella patelloides	78.705	619	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932785.1	s__Hyella disjuncta	77.673	490	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317575.1	s__Stanieria cyanosphaera	76.1738	181	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207195.1	s__Pleurocapsa sp015207195	76.0678	181	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756305.1	s__Myxosarcina sp000756305	76.0264	196	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Myxosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355455.1	s__Stanieria sp002355455	75.9956	173	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034765.1	s__Pleurocapsa sp012034765	75.9549	107	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	99.36	99.13	0.90	0.87	3	-
GCF_000332195.1	s__Pleurocapsa sp000332195	75.882	158	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207585.1	s__LEGE-06147 sp015207585	75.7506	95	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__LEGE-06147	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672865.1	s__SIO1D9 sp010672865	75.1253	65	1227	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__SIO1D9;g__SIO1D9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:49:23,429] [INFO] GTDB search result was written to OceanDNA-b16160/result_gtdb.tsv
[2023-03-16 03:49:23,429] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:49:23,430] [INFO] DFAST_QC result json was written to OceanDNA-b16160/dqc_result.json
[2023-03-16 03:49:23,430] [INFO] DFAST_QC completed!
[2023-03-16 03:49:23,430] [INFO] Total running time: 0h1m51s