[2023-03-18 07:54:29,699] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:29,699] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:29,700] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bcb2a7f-a9d5-498b-a150-b7a15a35acf9/dqc_reference
[2023-03-18 07:54:30,793] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:30,793] [INFO] Task started: Prodigal
[2023-03-18 07:54:30,793] [INFO] Running command: cat /var/lib/cwl/stg05d34874-cb0a-4d18-9958-3008a6953a73/OceanDNA-a4439.fa | prodigal -d OceanDNA-a4439/cds.fna -a OceanDNA-a4439/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:36,468] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:36,468] [INFO] Task started: HMMsearch
[2023-03-18 07:54:36,468] [INFO] Running command: hmmsearch --tblout OceanDNA-a4439/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bcb2a7f-a9d5-498b-a150-b7a15a35acf9/dqc_reference/reference_markers.hmm OceanDNA-a4439/protein.faa > /dev/null
[2023-03-18 07:54:36,632] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:36,633] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg05d34874-cb0a-4d18-9958-3008a6953a73/OceanDNA-a4439.fa]
[2023-03-18 07:54:36,661] [INFO] Query marker FASTA was written to OceanDNA-a4439/markers.fasta
[2023-03-18 07:54:36,661] [INFO] Task started: Blastn
[2023-03-18 07:54:36,661] [INFO] Running command: blastn -query OceanDNA-a4439/markers.fasta -db /var/lib/cwl/stg7bcb2a7f-a9d5-498b-a150-b7a15a35acf9/dqc_reference/reference_markers.fasta -out OceanDNA-a4439/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:37,095] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:37,096] [INFO] Selected 5 target genomes.
[2023-03-18 07:54:37,097] [INFO] Target genome list was writen to OceanDNA-a4439/target_genomes.txt
[2023-03-18 07:54:37,099] [INFO] Task started: fastANI
[2023-03-18 07:54:37,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d34874-cb0a-4d18-9958-3008a6953a73/OceanDNA-a4439.fa --refList OceanDNA-a4439/target_genomes.txt --output OceanDNA-a4439/fastani_result.tsv --threads 1
[2023-03-18 07:54:37,874] [INFO] Task succeeded: fastANI
[2023-03-18 07:54:37,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bcb2a7f-a9d5-498b-a150-b7a15a35acf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:54:37,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bcb2a7f-a9d5-498b-a150-b7a15a35acf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:54:37,875] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:54:37,875] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:54:37,875] [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
--------------------------------------------------------------------------------
[2023-03-18 07:54:37,876] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4439/tc_result.tsv
[2023-03-18 07:54:37,876] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:54:37,876] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:54:37,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bcb2a7f-a9d5-498b-a150-b7a15a35acf9/dqc_reference/checkm_data
[2023-03-18 07:54:37,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:54:37,927] [INFO] Task started: CheckM
[2023-03-18 07:54:37,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4439/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4439/checkm_input OceanDNA-a4439/checkm_result
[2023-03-18 07:54:58,354] [INFO] Task succeeded: CheckM
[2023-03-18 07:54:58,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:54:58,358] [INFO] ===== Completeness check finished =====
[2023-03-18 07:54:58,358] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:54:58,358] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4439/markers.fasta)
[2023-03-18 07:54:58,358] [INFO] Task started: Blastn
[2023-03-18 07:54:58,358] [INFO] Running command: blastn -query OceanDNA-a4439/markers.fasta -db /var/lib/cwl/stg7bcb2a7f-a9d5-498b-a150-b7a15a35acf9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4439/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:58,932] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:58,935] [INFO] Selected 8 target genomes.
[2023-03-18 07:54:58,935] [INFO] Target genome list was writen to OceanDNA-a4439/target_genomes_gtdb.txt
[2023-03-18 07:54:58,947] [INFO] Task started: fastANI
[2023-03-18 07:54:58,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d34874-cb0a-4d18-9958-3008a6953a73/OceanDNA-a4439.fa --refList OceanDNA-a4439/target_genomes_gtdb.txt --output OceanDNA-a4439/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:55:01,107] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:01,112] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:55:01,112] [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_002731195.1	s__MGIIb-O3 sp002731195	97.3784	258	355	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002172375.1	s__MGIIb-O3 sp002172375	82.4672	247	355	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712575.1	s__MGIIb-O3 sp002712575	81.9703	251	355	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719615.1	s__MGIIb-O3 sp002719615	81.5597	269	355	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602595.1	s__MGIIb-O3 sp003602595	81.5098	271	355	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457145.1	s__MGIIb-O3 sp002457145	80.2368	257	355	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.76	99.72	0.89	0.85	3	-
GCA_002503285.1	s__MGIIb-O3 sp002503285	77.1738	101	355	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.00	95.68	0.94	0.92	11	-
--------------------------------------------------------------------------------
[2023-03-18 07:55:01,113] [INFO] GTDB search result was written to OceanDNA-a4439/result_gtdb.tsv
[2023-03-18 07:55:01,114] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:55:01,116] [INFO] DFAST_QC result json was written to OceanDNA-a4439/dqc_result.json
[2023-03-18 07:55:01,116] [INFO] DFAST_QC completed!
[2023-03-18 07:55:01,116] [INFO] Total running time: 0h0m31s