[2023-03-15 18:39:12,307] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,307] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg87fbb6c0-f9c5-45c7-9d49-6a81066b4c73/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,657] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,657] [INFO] Running command: cat /var/lib/cwl/stg19000e33-e190-4181-a12f-86d9855c8550/OceanDNA-a2148.fa | prodigal -d OceanDNA-a2148/cds.fna -a OceanDNA-a2148/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:19,054] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:19,055] [INFO] Task started: HMMsearch
[2023-03-15 18:39:19,055] [INFO] Running command: hmmsearch --tblout OceanDNA-a2148/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87fbb6c0-f9c5-45c7-9d49-6a81066b4c73/dqc_reference/reference_markers.hmm OceanDNA-a2148/protein.faa > /dev/null
[2023-03-15 18:39:19,211] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:19,212] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg19000e33-e190-4181-a12f-86d9855c8550/OceanDNA-a2148.fa]
[2023-03-15 18:39:19,222] [INFO] Query marker FASTA was written to OceanDNA-a2148/markers.fasta
[2023-03-15 18:39:19,222] [INFO] Task started: Blastn
[2023-03-15 18:39:19,222] [INFO] Running command: blastn -query OceanDNA-a2148/markers.fasta -db /var/lib/cwl/stg87fbb6c0-f9c5-45c7-9d49-6a81066b4c73/dqc_reference/reference_markers.fasta -out OceanDNA-a2148/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:19,669] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:19,670] [INFO] Selected 6 target genomes.
[2023-03-15 18:39:19,670] [INFO] Target genome list was writen to OceanDNA-a2148/target_genomes.txt
[2023-03-15 18:39:19,673] [INFO] Task started: fastANI
[2023-03-15 18:39:19,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg19000e33-e190-4181-a12f-86d9855c8550/OceanDNA-a2148.fa --refList OceanDNA-a2148/target_genomes.txt --output OceanDNA-a2148/fastani_result.tsv --threads 1
[2023-03-15 18:39:21,912] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:21,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87fbb6c0-f9c5-45c7-9d49-6a81066b4c73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:21,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87fbb6c0-f9c5-45c7-9d49-6a81066b4c73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:21,913] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:21,913] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:21,913] [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 18:39:21,913] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2148/tc_result.tsv
[2023-03-15 18:39:21,913] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:21,913] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:21,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87fbb6c0-f9c5-45c7-9d49-6a81066b4c73/dqc_reference/checkm_data
[2023-03-15 18:39:21,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:21,918] [INFO] Task started: CheckM
[2023-03-15 18:39:21,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2148/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2148/checkm_input OceanDNA-a2148/checkm_result
[2023-03-15 18:39:47,203] [INFO] Task succeeded: CheckM
[2023-03-15 18:39:47,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:39:47,205] [INFO] ===== Completeness check finished =====
[2023-03-15 18:39:47,205] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:39:47,206] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2148/markers.fasta)
[2023-03-15 18:39:47,206] [INFO] Task started: Blastn
[2023-03-15 18:39:47,206] [INFO] Running command: blastn -query OceanDNA-a2148/markers.fasta -db /var/lib/cwl/stg87fbb6c0-f9c5-45c7-9d49-6a81066b4c73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2148/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:49,469] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:49,470] [INFO] Selected 10 target genomes.
[2023-03-15 18:39:49,470] [INFO] Target genome list was writen to OceanDNA-a2148/target_genomes_gtdb.txt
[2023-03-15 18:39:49,784] [INFO] Task started: fastANI
[2023-03-15 18:39:49,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg19000e33-e190-4181-a12f-86d9855c8550/OceanDNA-a2148.fa --refList OceanDNA-a2148/target_genomes_gtdb.txt --output OceanDNA-a2148/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:39:52,747] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:52,750] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:39:52,751] [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_002688825.1	s__MGIIa-L1 sp002688825	77.25	71	310	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_009887195.1	s__MGIIa-L1 sp009887195	77.0319	86	310	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_002702945.1	s__MGIIa-L1 sp002702945	76.8772	52	310	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.55	98.53	0.86	0.86	3	-
GCA_002726395.1	s__MGIIa-L1 sp002726395	76.8737	76	310	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_003602575.1	s__MGIIa-L1 sp003602575	76.4202	59	310	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:39:52,751] [INFO] GTDB search result was written to OceanDNA-a2148/result_gtdb.tsv
[2023-03-15 18:39:52,751] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:39:52,752] [INFO] DFAST_QC result json was written to OceanDNA-a2148/dqc_result.json
[2023-03-15 18:39:52,752] [INFO] DFAST_QC completed!
[2023-03-15 18:39:52,752] [INFO] Total running time: 0h0m40s