[2023-03-18 04:04:53,880] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,880] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f84defd-2b62-48f9-881f-c37fc9d5af6e/dqc_reference
[2023-03-18 04:04:55,039] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,039] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,039] [INFO] Running command: cat /var/lib/cwl/stg5b655354-9795-4286-a4c5-066924c62324/OceanDNA-a4842.fa | prodigal -d OceanDNA-a4842/cds.fna -a OceanDNA-a4842/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:00,735] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:00,736] [INFO] Task started: HMMsearch
[2023-03-18 04:05:00,736] [INFO] Running command: hmmsearch --tblout OceanDNA-a4842/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f84defd-2b62-48f9-881f-c37fc9d5af6e/dqc_reference/reference_markers.hmm OceanDNA-a4842/protein.faa > /dev/null
[2023-03-18 04:05:00,895] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:00,896] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5b655354-9795-4286-a4c5-066924c62324/OceanDNA-a4842.fa]
[2023-03-18 04:05:00,905] [INFO] Query marker FASTA was written to OceanDNA-a4842/markers.fasta
[2023-03-18 04:05:00,905] [INFO] Task started: Blastn
[2023-03-18 04:05:00,905] [INFO] Running command: blastn -query OceanDNA-a4842/markers.fasta -db /var/lib/cwl/stg2f84defd-2b62-48f9-881f-c37fc9d5af6e/dqc_reference/reference_markers.fasta -out OceanDNA-a4842/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:01,322] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:01,323] [INFO] Selected 2 target genomes.
[2023-03-18 04:05:01,323] [INFO] Target genome list was writen to OceanDNA-a4842/target_genomes.txt
[2023-03-18 04:05:01,324] [INFO] Task started: fastANI
[2023-03-18 04:05:01,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b655354-9795-4286-a4c5-066924c62324/OceanDNA-a4842.fa --refList OceanDNA-a4842/target_genomes.txt --output OceanDNA-a4842/fastani_result.tsv --threads 1
[2023-03-18 04:05:01,830] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:01,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f84defd-2b62-48f9-881f-c37fc9d5af6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:01,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f84defd-2b62-48f9-881f-c37fc9d5af6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:01,830] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:05:01,830] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:05:01,830] [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 04:05:01,831] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4842/tc_result.tsv
[2023-03-18 04:05:01,831] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:01,831] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:01,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f84defd-2b62-48f9-881f-c37fc9d5af6e/dqc_reference/checkm_data
[2023-03-18 04:05:01,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:02,153] [INFO] Task started: CheckM
[2023-03-18 04:05:02,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4842/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4842/checkm_input OceanDNA-a4842/checkm_result
[2023-03-18 04:05:22,435] [INFO] Task succeeded: CheckM
[2023-03-18 04:05:22,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.99%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:05:22,437] [INFO] ===== Completeness check finished =====
[2023-03-18 04:05:22,437] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:05:22,437] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4842/markers.fasta)
[2023-03-18 04:05:22,437] [INFO] Task started: Blastn
[2023-03-18 04:05:22,437] [INFO] Running command: blastn -query OceanDNA-a4842/markers.fasta -db /var/lib/cwl/stg2f84defd-2b62-48f9-881f-c37fc9d5af6e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4842/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:22,851] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:22,852] [INFO] Selected 7 target genomes.
[2023-03-18 04:05:22,852] [INFO] Target genome list was writen to OceanDNA-a4842/target_genomes_gtdb.txt
[2023-03-18 04:05:23,042] [INFO] Task started: fastANI
[2023-03-18 04:05:23,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b655354-9795-4286-a4c5-066924c62324/OceanDNA-a4842.fa --refList OceanDNA-a4842/target_genomes_gtdb.txt --output OceanDNA-a4842/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:05:24,775] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:24,780] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:05:24,780] [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_002727275.1	s__Thalassarchaeum sp002727275	82.4874	246	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503055.1	s__Thalassarchaeum sp002503055	81.863	208	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.71	99.22	0.93	0.84	5	-
GCA_002501885.1	s__Thalassarchaeum sp002501885	81.5585	204	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.85	97.05	0.83	0.68	9	-
GCA_002714745.1	s__Thalassarchaeum sp002714745	79.9996	170	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	97.82	95.69	0.77	0.69	7	-
GCA_002698225.1	s__Thalassarchaeum sp002698225	79.1001	154	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.66	99.66	0.83	0.83	2	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	76.78	59	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195715.1	s__Thalassarchaeum sp004195715	76.7688	58	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-18 04:05:24,780] [INFO] GTDB search result was written to OceanDNA-a4842/result_gtdb.tsv
[2023-03-18 04:05:24,780] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:05:24,781] [INFO] DFAST_QC result json was written to OceanDNA-a4842/dqc_result.json
[2023-03-18 04:05:24,781] [INFO] DFAST_QC completed!
[2023-03-18 04:05:24,781] [INFO] Total running time: 0h0m31s