[2023-03-15 13:20:53,731] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:53,731] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:53,731] [INFO] DQC Reference Directory: /var/lib/cwl/stge60639a0-4239-4a15-b379-564e5647feec/dqc_reference
[2023-03-15 13:20:54,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:54,907] [INFO] Task started: Prodigal
[2023-03-15 13:20:54,907] [INFO] Running command: cat /var/lib/cwl/stg8db75b07-41a6-49be-9451-2ad708c95206/OceanDNA-b17332.fa | prodigal -d OceanDNA-b17332/cds.fna -a OceanDNA-b17332/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:05,187] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:05,187] [INFO] Task started: HMMsearch
[2023-03-15 13:21:05,188] [INFO] Running command: hmmsearch --tblout OceanDNA-b17332/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge60639a0-4239-4a15-b379-564e5647feec/dqc_reference/reference_markers.hmm OceanDNA-b17332/protein.faa > /dev/null
[2023-03-15 13:21:05,422] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:05,423] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8db75b07-41a6-49be-9451-2ad708c95206/OceanDNA-b17332.fa]
[2023-03-15 13:21:05,440] [INFO] Query marker FASTA was written to OceanDNA-b17332/markers.fasta
[2023-03-15 13:21:05,441] [INFO] Task started: Blastn
[2023-03-15 13:21:05,441] [INFO] Running command: blastn -query OceanDNA-b17332/markers.fasta -db /var/lib/cwl/stge60639a0-4239-4a15-b379-564e5647feec/dqc_reference/reference_markers.fasta -out OceanDNA-b17332/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:06,174] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:06,176] [INFO] Selected 26 target genomes.
[2023-03-15 13:21:06,176] [INFO] Target genome list was writen to OceanDNA-b17332/target_genomes.txt
[2023-03-15 13:21:06,198] [INFO] Task started: fastANI
[2023-03-15 13:21:06,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg8db75b07-41a6-49be-9451-2ad708c95206/OceanDNA-b17332.fa --refList OceanDNA-b17332/target_genomes.txt --output OceanDNA-b17332/fastani_result.tsv --threads 1
[2023-03-15 13:21:25,177] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:25,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge60639a0-4239-4a15-b379-564e5647feec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:25,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge60639a0-4239-4a15-b379-564e5647feec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:25,178] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:25,178] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:21:25,178] [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 13:21:25,179] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17332/tc_result.tsv
[2023-03-15 13:21:25,179] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:25,179] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:25,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge60639a0-4239-4a15-b379-564e5647feec/dqc_reference/checkm_data
[2023-03-15 13:21:25,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:25,186] [INFO] Task started: CheckM
[2023-03-15 13:21:25,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17332/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17332/checkm_input OceanDNA-b17332/checkm_result
[2023-03-15 13:21:55,395] [INFO] Task succeeded: CheckM
[2023-03-15 13:21:55,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:21:55,398] [INFO] ===== Completeness check finished =====
[2023-03-15 13:21:55,398] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:21:55,398] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17332/markers.fasta)
[2023-03-15 13:21:55,399] [INFO] Task started: Blastn
[2023-03-15 13:21:55,399] [INFO] Running command: blastn -query OceanDNA-b17332/markers.fasta -db /var/lib/cwl/stge60639a0-4239-4a15-b379-564e5647feec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17332/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:56,599] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:56,600] [INFO] Selected 24 target genomes.
[2023-03-15 13:21:56,600] [INFO] Target genome list was writen to OceanDNA-b17332/target_genomes_gtdb.txt
[2023-03-15 13:21:56,625] [INFO] Task started: fastANI
[2023-03-15 13:21:56,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg8db75b07-41a6-49be-9451-2ad708c95206/OceanDNA-b17332.fa --refList OceanDNA-b17332/target_genomes_gtdb.txt --output OceanDNA-b17332/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:10,995] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:10,999] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:22:10,999] [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_002390225.1	s__UBA2589 sp002390225	78.334	213	504	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002885.1	s__UBA2589 sp013002885	76.6137	89	504	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
GCA_002348465.1	s__UBA2589 sp002348465	76.522	57	504	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	98.53	97.69	0.86	0.81	4	-
GCA_016873995.1	s__UBA2982 sp016873995	76.4785	52	504	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015664885.1	s__UBA1138 sp003447875	76.2831	53	504	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:10,999] [INFO] GTDB search result was written to OceanDNA-b17332/result_gtdb.tsv
[2023-03-15 13:22:11,000] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:11,001] [INFO] DFAST_QC result json was written to OceanDNA-b17332/dqc_result.json
[2023-03-15 13:22:11,001] [INFO] DFAST_QC completed!
[2023-03-15 13:22:11,001] [INFO] Total running time: 0h1m17s