[2023-03-15 17:46:31,492] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,492] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg53e1ec43-b606-438c-9bc7-7b2c57f6a1a6/dqc_reference
[2023-03-15 17:46:32,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,606] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,607] [INFO] Running command: cat /var/lib/cwl/stg044a72fb-cdaf-4fdd-93fd-cd2b000be05d/OceanDNA-a2127.fa | prodigal -d OceanDNA-a2127/cds.fna -a OceanDNA-a2127/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:38,696] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:38,696] [INFO] Task started: HMMsearch
[2023-03-15 17:46:38,696] [INFO] Running command: hmmsearch --tblout OceanDNA-a2127/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53e1ec43-b606-438c-9bc7-7b2c57f6a1a6/dqc_reference/reference_markers.hmm OceanDNA-a2127/protein.faa > /dev/null
[2023-03-15 17:46:38,908] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:38,909] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg044a72fb-cdaf-4fdd-93fd-cd2b000be05d/OceanDNA-a2127.fa]
[2023-03-15 17:46:38,925] [INFO] Query marker FASTA was written to OceanDNA-a2127/markers.fasta
[2023-03-15 17:46:38,926] [INFO] Task started: Blastn
[2023-03-15 17:46:38,926] [INFO] Running command: blastn -query OceanDNA-a2127/markers.fasta -db /var/lib/cwl/stg53e1ec43-b606-438c-9bc7-7b2c57f6a1a6/dqc_reference/reference_markers.fasta -out OceanDNA-a2127/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:39,387] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:39,389] [INFO] Selected 6 target genomes.
[2023-03-15 17:46:39,390] [INFO] Target genome list was writen to OceanDNA-a2127/target_genomes.txt
[2023-03-15 17:46:39,394] [INFO] Task started: fastANI
[2023-03-15 17:46:39,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg044a72fb-cdaf-4fdd-93fd-cd2b000be05d/OceanDNA-a2127.fa --refList OceanDNA-a2127/target_genomes.txt --output OceanDNA-a2127/fastani_result.tsv --threads 1
[2023-03-15 17:46:41,218] [INFO] Task succeeded: fastANI
[2023-03-15 17:46:41,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53e1ec43-b606-438c-9bc7-7b2c57f6a1a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:46:41,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53e1ec43-b606-438c-9bc7-7b2c57f6a1a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:46:41,219] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:46:41,219] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:46:41,219] [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
--------------------------------------------------------------------------------
[2023-03-15 17:46:41,221] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2127/tc_result.tsv
[2023-03-15 17:46:41,221] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:46:41,221] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:46:41,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53e1ec43-b606-438c-9bc7-7b2c57f6a1a6/dqc_reference/checkm_data
[2023-03-15 17:46:41,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:46:41,229] [INFO] Task started: CheckM
[2023-03-15 17:46:41,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2127/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2127/checkm_input OceanDNA-a2127/checkm_result
[2023-03-15 17:47:02,387] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:02,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:02,392] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:02,392] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:02,392] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2127/markers.fasta)
[2023-03-15 17:47:02,394] [INFO] Task started: Blastn
[2023-03-15 17:47:02,394] [INFO] Running command: blastn -query OceanDNA-a2127/markers.fasta -db /var/lib/cwl/stg53e1ec43-b606-438c-9bc7-7b2c57f6a1a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2127/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:02,880] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:02,882] [INFO] Selected 6 target genomes.
[2023-03-15 17:47:02,882] [INFO] Target genome list was writen to OceanDNA-a2127/target_genomes_gtdb.txt
[2023-03-15 17:47:02,892] [INFO] Task started: fastANI
[2023-03-15 17:47:02,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg044a72fb-cdaf-4fdd-93fd-cd2b000be05d/OceanDNA-a2127.fa --refList OceanDNA-a2127/target_genomes_gtdb.txt --output OceanDNA-a2127/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:04,868] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:04,873] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:47:04,873] [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_013329925.1	s__MGIIa-L1 sp8734u	93.1877	238	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_002688825.1	s__MGIIa-L1 sp002688825	87.8422	194	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726395.1	s__MGIIa-L1 sp002726395	86.2028	248	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.39	99.39	0.85	0.85	2	-
GCA_009887195.1	s__MGIIa-L1 sp009887195	85.1852	245	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.91	98.88	0.90	0.86	3	-
GCA_018659375.1	s__MGIIa-L1 sp018659375	84.4875	277	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.68	99.68	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:04,874] [INFO] GTDB search result was written to OceanDNA-a2127/result_gtdb.tsv
[2023-03-15 17:47:04,874] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:04,876] [INFO] DFAST_QC result json was written to OceanDNA-a2127/dqc_result.json
[2023-03-15 17:47:04,876] [INFO] DFAST_QC completed!
[2023-03-15 17:47:04,876] [INFO] Total running time: 0h0m33s