[2023-03-17 05:59:11,049] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:11,049] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:11,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg40c171bb-49e6-44df-ba7f-4ca8de3b4632/dqc_reference
[2023-03-17 05:59:12,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:12,175] [INFO] Task started: Prodigal
[2023-03-17 05:59:12,176] [INFO] Running command: cat /var/lib/cwl/stg952dbc06-c11d-4f65-8489-df32af256fca/OceanDNA-a4078.fa | prodigal -d OceanDNA-a4078/cds.fna -a OceanDNA-a4078/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:19,564] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:19,564] [INFO] Task started: HMMsearch
[2023-03-17 05:59:19,565] [INFO] Running command: hmmsearch --tblout OceanDNA-a4078/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40c171bb-49e6-44df-ba7f-4ca8de3b4632/dqc_reference/reference_markers.hmm OceanDNA-a4078/protein.faa > /dev/null
[2023-03-17 05:59:19,698] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:19,699] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg952dbc06-c11d-4f65-8489-df32af256fca/OceanDNA-a4078.fa]
[2023-03-17 05:59:19,710] [INFO] Query marker FASTA was written to OceanDNA-a4078/markers.fasta
[2023-03-17 05:59:19,710] [INFO] Task started: Blastn
[2023-03-17 05:59:19,710] [INFO] Running command: blastn -query OceanDNA-a4078/markers.fasta -db /var/lib/cwl/stg40c171bb-49e6-44df-ba7f-4ca8de3b4632/dqc_reference/reference_markers.fasta -out OceanDNA-a4078/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:20,142] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:20,142] [INFO] Selected 5 target genomes.
[2023-03-17 05:59:20,143] [INFO] Target genome list was writen to OceanDNA-a4078/target_genomes.txt
[2023-03-17 05:59:20,145] [INFO] Task started: fastANI
[2023-03-17 05:59:20,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg952dbc06-c11d-4f65-8489-df32af256fca/OceanDNA-a4078.fa --refList OceanDNA-a4078/target_genomes.txt --output OceanDNA-a4078/fastani_result.tsv --threads 1
[2023-03-17 05:59:21,230] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:21,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40c171bb-49e6-44df-ba7f-4ca8de3b4632/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:21,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40c171bb-49e6-44df-ba7f-4ca8de3b4632/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:21,231] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:21,231] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:59:21,231] [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
--------------------------------------------------------------------------------
[2023-03-17 05:59:21,231] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4078/tc_result.tsv
[2023-03-17 05:59:21,231] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:21,232] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:21,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40c171bb-49e6-44df-ba7f-4ca8de3b4632/dqc_reference/checkm_data
[2023-03-17 05:59:21,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:21,237] [INFO] Task started: CheckM
[2023-03-17 05:59:21,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4078/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4078/checkm_input OceanDNA-a4078/checkm_result
[2023-03-17 05:59:44,568] [INFO] Task succeeded: CheckM
[2023-03-17 05:59:44,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:59:44,570] [INFO] ===== Completeness check finished =====
[2023-03-17 05:59:44,570] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:59:44,570] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4078/markers.fasta)
[2023-03-17 05:59:44,571] [INFO] Task started: Blastn
[2023-03-17 05:59:44,571] [INFO] Running command: blastn -query OceanDNA-a4078/markers.fasta -db /var/lib/cwl/stg40c171bb-49e6-44df-ba7f-4ca8de3b4632/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4078/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:44,966] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:44,967] [INFO] Selected 8 target genomes.
[2023-03-17 05:59:44,967] [INFO] Target genome list was writen to OceanDNA-a4078/target_genomes_gtdb.txt
[2023-03-17 05:59:45,074] [INFO] Task started: fastANI
[2023-03-17 05:59:45,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg952dbc06-c11d-4f65-8489-df32af256fca/OceanDNA-a4078.fa --refList OceanDNA-a4078/target_genomes_gtdb.txt --output OceanDNA-a4078/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:59:47,000] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:47,003] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:59:47,003] [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_002503285.1	s__MGIIb-O3 sp002503285	93.6333	428	460	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.00	95.68	0.94	0.92	11	-
GCA_002457145.1	s__MGIIb-O3 sp002457145	76.9806	127	460	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_002731195.1	s__MGIIb-O3 sp002731195	76.7785	118	460	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_016777225.1	s__MGIIb-O2 sp016777225	76.4435	70	460	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:59:47,003] [INFO] GTDB search result was written to OceanDNA-a4078/result_gtdb.tsv
[2023-03-17 05:59:47,004] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:59:47,004] [INFO] DFAST_QC result json was written to OceanDNA-a4078/dqc_result.json
[2023-03-17 05:59:47,004] [INFO] DFAST_QC completed!
[2023-03-17 05:59:47,004] [INFO] Total running time: 0h0m36s