[2023-03-18 23:22:48,489] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:22:48,489] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:22:48,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg3acd32d5-4816-4da9-985e-85b8e27e3fec/dqc_reference
[2023-03-18 23:22:49,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:22:49,618] [INFO] Task started: Prodigal
[2023-03-18 23:22:49,619] [INFO] Running command: cat /var/lib/cwl/stg5ea748ef-1e9c-46bb-8baa-9394fdadb3eb/OceanDNA-a1840.fa | prodigal -d OceanDNA-a1840/cds.fna -a OceanDNA-a1840/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:22:56,844] [INFO] Task succeeded: Prodigal
[2023-03-18 23:22:56,844] [INFO] Task started: HMMsearch
[2023-03-18 23:22:56,844] [INFO] Running command: hmmsearch --tblout OceanDNA-a1840/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3acd32d5-4816-4da9-985e-85b8e27e3fec/dqc_reference/reference_markers.hmm OceanDNA-a1840/protein.faa > /dev/null
[2023-03-18 23:22:57,010] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:22:57,011] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5ea748ef-1e9c-46bb-8baa-9394fdadb3eb/OceanDNA-a1840.fa]
[2023-03-18 23:22:57,022] [INFO] Query marker FASTA was written to OceanDNA-a1840/markers.fasta
[2023-03-18 23:22:57,022] [INFO] Task started: Blastn
[2023-03-18 23:22:57,022] [INFO] Running command: blastn -query OceanDNA-a1840/markers.fasta -db /var/lib/cwl/stg3acd32d5-4816-4da9-985e-85b8e27e3fec/dqc_reference/reference_markers.fasta -out OceanDNA-a1840/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:22:57,449] [INFO] Task succeeded: Blastn
[2023-03-18 23:22:57,450] [INFO] Selected 6 target genomes.
[2023-03-18 23:22:57,451] [INFO] Target genome list was writen to OceanDNA-a1840/target_genomes.txt
[2023-03-18 23:22:57,455] [INFO] Task started: fastANI
[2023-03-18 23:22:57,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea748ef-1e9c-46bb-8baa-9394fdadb3eb/OceanDNA-a1840.fa --refList OceanDNA-a1840/target_genomes.txt --output OceanDNA-a1840/fastani_result.tsv --threads 1
[2023-03-18 23:23:00,406] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:00,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3acd32d5-4816-4da9-985e-85b8e27e3fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:23:00,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3acd32d5-4816-4da9-985e-85b8e27e3fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:23:00,406] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:23:00,406] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:23:00,407] [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 23:23:00,407] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1840/tc_result.tsv
[2023-03-18 23:23:00,407] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:23:00,407] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:23:00,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3acd32d5-4816-4da9-985e-85b8e27e3fec/dqc_reference/checkm_data
[2023-03-18 23:23:00,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:23:00,413] [INFO] Task started: CheckM
[2023-03-18 23:23:00,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1840/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1840/checkm_input OceanDNA-a1840/checkm_result
[2023-03-18 23:23:23,521] [INFO] Task succeeded: CheckM
[2023-03-18 23:23:23,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:23:23,525] [INFO] ===== Completeness check finished =====
[2023-03-18 23:23:23,525] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:23:23,525] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1840/markers.fasta)
[2023-03-18 23:23:23,526] [INFO] Task started: Blastn
[2023-03-18 23:23:23,527] [INFO] Running command: blastn -query OceanDNA-a1840/markers.fasta -db /var/lib/cwl/stg3acd32d5-4816-4da9-985e-85b8e27e3fec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1840/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:23:23,959] [INFO] Task succeeded: Blastn
[2023-03-18 23:23:23,960] [INFO] Selected 10 target genomes.
[2023-03-18 23:23:23,960] [INFO] Target genome list was writen to OceanDNA-a1840/target_genomes_gtdb.txt
[2023-03-18 23:23:23,965] [INFO] Task started: fastANI
[2023-03-18 23:23:23,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea748ef-1e9c-46bb-8baa-9394fdadb3eb/OceanDNA-a1840.fa --refList OceanDNA-a1840/target_genomes_gtdb.txt --output OceanDNA-a1840/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:23:27,177] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:27,182] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:23:27,182] [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_002696315.1	s__MGIIa-I sp002696315	99.4352	419	467	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	99.61	99.61	0.93	0.93	2	conclusive
GCA_002498205.1	s__MGIIa-I sp002498205	84.4676	269	467	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692465.1	s__MGIIa-I sp002692465	82.4517	313	467	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720275.1	s__MGIIa-I sp002720275	81.8902	364	467	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	98.73	98.73	0.82	0.82	2	-
GCA_002699515.1	s__MGIIa-I sp002699515	79.0853	228	467	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720095.2	s__MGIIa-I sp002720095	78.5826	184	467	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	99.78	99.77	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-18 23:23:27,182] [INFO] GTDB search result was written to OceanDNA-a1840/result_gtdb.tsv
[2023-03-18 23:23:27,183] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:23:27,184] [INFO] DFAST_QC result json was written to OceanDNA-a1840/dqc_result.json
[2023-03-18 23:23:27,184] [INFO] DFAST_QC completed!
[2023-03-18 23:23:27,184] [INFO] Total running time: 0h0m39s