[2023-03-16 10:35:17,571] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:35:17,571] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:35:17,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg3dc6392b-3c81-4c46-8e7a-326a48d11509/dqc_reference
[2023-03-16 10:35:18,686] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:35:18,687] [INFO] Task started: Prodigal
[2023-03-16 10:35:18,687] [INFO] Running command: cat /var/lib/cwl/stge4505bce-bf81-42ba-8416-949e553c1f69/OceanDNA-b14214.fa | prodigal -d OceanDNA-b14214/cds.fna -a OceanDNA-b14214/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:35:28,145] [INFO] Task succeeded: Prodigal
[2023-03-16 10:35:28,145] [INFO] Task started: HMMsearch
[2023-03-16 10:35:28,145] [INFO] Running command: hmmsearch --tblout OceanDNA-b14214/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3dc6392b-3c81-4c46-8e7a-326a48d11509/dqc_reference/reference_markers.hmm OceanDNA-b14214/protein.faa > /dev/null
[2023-03-16 10:35:28,337] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:35:28,337] [INFO] Found 6/6 markers.
[2023-03-16 10:35:28,351] [INFO] Query marker FASTA was written to OceanDNA-b14214/markers.fasta
[2023-03-16 10:35:28,352] [INFO] Task started: Blastn
[2023-03-16 10:35:28,352] [INFO] Running command: blastn -query OceanDNA-b14214/markers.fasta -db /var/lib/cwl/stg3dc6392b-3c81-4c46-8e7a-326a48d11509/dqc_reference/reference_markers.fasta -out OceanDNA-b14214/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:35:28,854] [INFO] Task succeeded: Blastn
[2023-03-16 10:35:28,854] [INFO] Selected 5 target genomes.
[2023-03-16 10:35:28,855] [INFO] Target genome list was writen to OceanDNA-b14214/target_genomes.txt
[2023-03-16 10:35:28,858] [INFO] Task started: fastANI
[2023-03-16 10:35:28,858] [INFO] Running command: fastANI --query /var/lib/cwl/stge4505bce-bf81-42ba-8416-949e553c1f69/OceanDNA-b14214.fa --refList OceanDNA-b14214/target_genomes.txt --output OceanDNA-b14214/fastani_result.tsv --threads 1
[2023-03-16 10:35:31,094] [INFO] Task succeeded: fastANI
[2023-03-16 10:35:31,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3dc6392b-3c81-4c46-8e7a-326a48d11509/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:35:31,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3dc6392b-3c81-4c46-8e7a-326a48d11509/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:35:31,095] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:35:31,095] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:35:31,095] [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
--------------------------------------------------------------------------------
[2023-03-16 10:35:31,095] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14214/tc_result.tsv
[2023-03-16 10:35:31,095] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:35:31,095] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:35:31,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3dc6392b-3c81-4c46-8e7a-326a48d11509/dqc_reference/checkm_data
[2023-03-16 10:35:31,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:35:31,106] [INFO] Task started: CheckM
[2023-03-16 10:35:31,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14214/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14214/checkm_input OceanDNA-b14214/checkm_result
[2023-03-16 10:36:02,316] [INFO] Task succeeded: CheckM
[2023-03-16 10:36:02,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:36:02,318] [INFO] ===== Completeness check finished =====
[2023-03-16 10:36:02,319] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:36:02,319] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14214/markers.fasta)
[2023-03-16 10:36:02,319] [INFO] Task started: Blastn
[2023-03-16 10:36:02,319] [INFO] Running command: blastn -query OceanDNA-b14214/markers.fasta -db /var/lib/cwl/stg3dc6392b-3c81-4c46-8e7a-326a48d11509/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14214/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:36:03,042] [INFO] Task succeeded: Blastn
[2023-03-16 10:36:03,042] [INFO] Selected 10 target genomes.
[2023-03-16 10:36:03,043] [INFO] Target genome list was writen to OceanDNA-b14214/target_genomes_gtdb.txt
[2023-03-16 10:36:03,057] [INFO] Task started: fastANI
[2023-03-16 10:36:03,057] [INFO] Running command: fastANI --query /var/lib/cwl/stge4505bce-bf81-42ba-8416-949e553c1f69/OceanDNA-b14214.fa --refList OceanDNA-b14214/target_genomes_gtdb.txt --output OceanDNA-b14214/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:36:06,679] [INFO] Task succeeded: fastANI
[2023-03-16 10:36:06,684] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:36:06,684] [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_008373095.1	s__UBA11996 sp002320875	87.631	462	548	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	99.51	99.45	0.90	0.90	3	-
GCA_002728195.1	s__UBA11996 sp002728195	83.6357	381	548	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722155.1	s__UBA11996 sp002722155	81.8073	275	548	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	99.59	99.59	0.67	0.67	2	-
GCA_002500485.1	s__UBA11996 sp002500485	80.0333	201	548	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228105.1	s__UBA11996 sp003228105	78.1914	143	548	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012965485.1	s__UBA11996 sp012965485	77.1753	91	548	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:36:06,684] [INFO] GTDB search result was written to OceanDNA-b14214/result_gtdb.tsv
[2023-03-16 10:36:06,684] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:36:06,685] [INFO] DFAST_QC result json was written to OceanDNA-b14214/dqc_result.json
[2023-03-16 10:36:06,685] [INFO] DFAST_QC completed!
[2023-03-16 10:36:06,685] [INFO] Total running time: 0h0m49s