[2023-03-17 13:01:51,372] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,373] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,373] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fcc1d62-4aad-4cbe-91b5-9b1254ec0416/dqc_reference
[2023-03-17 13:01:52,638] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,651] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,651] [INFO] Running command: cat /var/lib/cwl/stg0a54fc55-00eb-4ac1-b98f-b1de0db078ee/OceanDNA-b15831.fa | prodigal -d OceanDNA-b15831/cds.fna -a OceanDNA-b15831/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:05,927] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:05,927] [INFO] Task started: HMMsearch
[2023-03-17 13:02:05,927] [INFO] Running command: hmmsearch --tblout OceanDNA-b15831/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fcc1d62-4aad-4cbe-91b5-9b1254ec0416/dqc_reference/reference_markers.hmm OceanDNA-b15831/protein.faa > /dev/null
[2023-03-17 13:02:06,128] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:06,129] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0a54fc55-00eb-4ac1-b98f-b1de0db078ee/OceanDNA-b15831.fa]
[2023-03-17 13:02:06,147] [INFO] Query marker FASTA was written to OceanDNA-b15831/markers.fasta
[2023-03-17 13:02:06,147] [INFO] Task started: Blastn
[2023-03-17 13:02:06,147] [INFO] Running command: blastn -query OceanDNA-b15831/markers.fasta -db /var/lib/cwl/stg5fcc1d62-4aad-4cbe-91b5-9b1254ec0416/dqc_reference/reference_markers.fasta -out OceanDNA-b15831/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:06,739] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:06,740] [INFO] Selected 20 target genomes.
[2023-03-17 13:02:06,740] [INFO] Target genome list was writen to OceanDNA-b15831/target_genomes.txt
[2023-03-17 13:02:06,751] [INFO] Task started: fastANI
[2023-03-17 13:02:06,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a54fc55-00eb-4ac1-b98f-b1de0db078ee/OceanDNA-b15831.fa --refList OceanDNA-b15831/target_genomes.txt --output OceanDNA-b15831/fastani_result.tsv --threads 1
[2023-03-17 13:02:23,162] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:23,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fcc1d62-4aad-4cbe-91b5-9b1254ec0416/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:23,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fcc1d62-4aad-4cbe-91b5-9b1254ec0416/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:23,163] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:23,163] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:23,163] [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 13:02:23,163] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15831/tc_result.tsv
[2023-03-17 13:02:23,163] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:23,163] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:23,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fcc1d62-4aad-4cbe-91b5-9b1254ec0416/dqc_reference/checkm_data
[2023-03-17 13:02:23,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:23,170] [INFO] Task started: CheckM
[2023-03-17 13:02:23,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15831/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15831/checkm_input OceanDNA-b15831/checkm_result
[2023-03-17 13:02:58,589] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:58,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:58,591] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:58,592] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:58,592] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15831/markers.fasta)
[2023-03-17 13:02:58,592] [INFO] Task started: Blastn
[2023-03-17 13:02:58,592] [INFO] Running command: blastn -query OceanDNA-b15831/markers.fasta -db /var/lib/cwl/stg5fcc1d62-4aad-4cbe-91b5-9b1254ec0416/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15831/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:59,438] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:59,439] [INFO] Selected 11 target genomes.
[2023-03-17 13:02:59,439] [INFO] Target genome list was writen to OceanDNA-b15831/target_genomes_gtdb.txt
[2023-03-17 13:02:59,874] [INFO] Task started: fastANI
[2023-03-17 13:02:59,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a54fc55-00eb-4ac1-b98f-b1de0db078ee/OceanDNA-b15831.fa --refList OceanDNA-b15831/target_genomes_gtdb.txt --output OceanDNA-b15831/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:06,149] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:06,156] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:03:06,156] [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_002721995.1	s__UBA9611 sp002721995	98.5832	603	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	conclusive
GCA_002816575.1	s__UBA9611 sp002816575	79.7823	315	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328185.1	s__UBA9611 sp002328185	79.1977	424	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_013204585.1	s__UBA9611 sp013204585	79.0624	418	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746355.1	s__UBA9611 sp002746355	78.9057	427	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_002816585.1	s__UBA9611 sp002816585	78.6062	286	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392095.1	s__UBA9611 sp009391975	78.4569	296	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	-
GCA_002730485.1	s__UBA9611 sp002730485	77.8923	294	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959605.1	s__UBA9611 sp012959605	77.739	273	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.56	99.56	0.90	0.90	2	-
GCA_009840175.1	s__VXOI01 sp009840175	77.1997	214	684	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__VXOI01	95.0	99.70	99.70	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:06,156] [INFO] GTDB search result was written to OceanDNA-b15831/result_gtdb.tsv
[2023-03-17 13:03:06,157] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:06,157] [INFO] DFAST_QC result json was written to OceanDNA-b15831/dqc_result.json
[2023-03-17 13:03:06,158] [INFO] DFAST_QC completed!
[2023-03-17 13:03:06,158] [INFO] Total running time: 0h1m15s