[2023-03-16 16:43:21,786] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:43:21,786] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:43:21,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg55625902-56b5-4319-a696-37d844a5517a/dqc_reference
[2023-03-16 16:43:24,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:43:24,606] [INFO] Task started: Prodigal
[2023-03-16 16:43:24,606] [INFO] Running command: cat /var/lib/cwl/stg11365523-40f8-49ac-87ca-bf49dff251d2/OceanDNA-b14300.fa | prodigal -d OceanDNA-b14300/cds.fna -a OceanDNA-b14300/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:43:35,508] [INFO] Task succeeded: Prodigal
[2023-03-16 16:43:35,508] [INFO] Task started: HMMsearch
[2023-03-16 16:43:35,508] [INFO] Running command: hmmsearch --tblout OceanDNA-b14300/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55625902-56b5-4319-a696-37d844a5517a/dqc_reference/reference_markers.hmm OceanDNA-b14300/protein.faa > /dev/null
[2023-03-16 16:43:35,768] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:43:35,769] [INFO] Found 6/6 markers.
[2023-03-16 16:43:35,786] [INFO] Query marker FASTA was written to OceanDNA-b14300/markers.fasta
[2023-03-16 16:43:35,791] [INFO] Task started: Blastn
[2023-03-16 16:43:35,791] [INFO] Running command: blastn -query OceanDNA-b14300/markers.fasta -db /var/lib/cwl/stg55625902-56b5-4319-a696-37d844a5517a/dqc_reference/reference_markers.fasta -out OceanDNA-b14300/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:43:36,667] [INFO] Task succeeded: Blastn
[2023-03-16 16:43:36,668] [INFO] Selected 7 target genomes.
[2023-03-16 16:43:36,668] [INFO] Target genome list was writen to OceanDNA-b14300/target_genomes.txt
[2023-03-16 16:43:36,703] [INFO] Task started: fastANI
[2023-03-16 16:43:36,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg11365523-40f8-49ac-87ca-bf49dff251d2/OceanDNA-b14300.fa --refList OceanDNA-b14300/target_genomes.txt --output OceanDNA-b14300/fastani_result.tsv --threads 1
[2023-03-16 16:43:39,401] [INFO] Task succeeded: fastANI
[2023-03-16 16:43:39,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55625902-56b5-4319-a696-37d844a5517a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:43:39,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55625902-56b5-4319-a696-37d844a5517a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:43:39,402] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:43:39,402] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:43:39,402] [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 16:43:39,402] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14300/tc_result.tsv
[2023-03-16 16:43:39,402] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:43:39,402] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:43:39,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55625902-56b5-4319-a696-37d844a5517a/dqc_reference/checkm_data
[2023-03-16 16:43:39,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:43:39,409] [INFO] Task started: CheckM
[2023-03-16 16:43:39,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14300/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14300/checkm_input OceanDNA-b14300/checkm_result
[2023-03-16 16:44:14,870] [INFO] Task succeeded: CheckM
[2023-03-16 16:44:14,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:44:14,873] [INFO] ===== Completeness check finished =====
[2023-03-16 16:44:14,873] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:44:14,873] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14300/markers.fasta)
[2023-03-16 16:44:14,874] [INFO] Task started: Blastn
[2023-03-16 16:44:14,874] [INFO] Running command: blastn -query OceanDNA-b14300/markers.fasta -db /var/lib/cwl/stg55625902-56b5-4319-a696-37d844a5517a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14300/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:44:15,580] [INFO] Task succeeded: Blastn
[2023-03-16 16:44:15,581] [INFO] Selected 5 target genomes.
[2023-03-16 16:44:15,581] [INFO] Target genome list was writen to OceanDNA-b14300/target_genomes_gtdb.txt
[2023-03-16 16:44:15,612] [INFO] Task started: fastANI
[2023-03-16 16:44:15,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg11365523-40f8-49ac-87ca-bf49dff251d2/OceanDNA-b14300.fa --refList OceanDNA-b14300/target_genomes_gtdb.txt --output OceanDNA-b14300/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:44:18,166] [INFO] Task succeeded: fastANI
[2023-03-16 16:44:18,170] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:44:18,171] [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_002435305.1	s__UBA11996 sp002435305	99.2786	536	623	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	99.14	98.93	0.85	0.82	4	conclusive
GCA_012965485.1	s__UBA11996 sp012965485	93.6094	329	623	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392675.1	s__UBA11996 sp009392675	89.6468	372	623	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	95.66	95.66	0.60	0.60	2	-
GCA_003228105.1	s__UBA11996 sp003228105	89.3439	427	623	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500485.1	s__UBA11996 sp002500485	87.1675	508	623	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 16:44:18,171] [INFO] GTDB search result was written to OceanDNA-b14300/result_gtdb.tsv
[2023-03-16 16:44:18,171] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:44:18,172] [INFO] DFAST_QC result json was written to OceanDNA-b14300/dqc_result.json
[2023-03-16 16:44:18,172] [INFO] DFAST_QC completed!
[2023-03-16 16:44:18,172] [INFO] Total running time: 0h0m56s