[2023-03-16 03:23:47,623] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:47,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:47,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c4355fe-1177-48bc-b394-6fc136ee767f/dqc_reference
[2023-03-16 03:23:49,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:49,415] [INFO] Task started: Prodigal
[2023-03-16 03:23:49,415] [INFO] Running command: cat /var/lib/cwl/stge4fc5534-2368-4a13-9a45-3da246f2684f/OceanDNA-b24739.fa | prodigal -d OceanDNA-b24739/cds.fna -a OceanDNA-b24739/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:23:57,959] [INFO] Task succeeded: Prodigal
[2023-03-16 03:23:57,960] [INFO] Task started: HMMsearch
[2023-03-16 03:23:57,960] [INFO] Running command: hmmsearch --tblout OceanDNA-b24739/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c4355fe-1177-48bc-b394-6fc136ee767f/dqc_reference/reference_markers.hmm OceanDNA-b24739/protein.faa > /dev/null
[2023-03-16 03:23:58,150] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:23:58,150] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge4fc5534-2368-4a13-9a45-3da246f2684f/OceanDNA-b24739.fa]
[2023-03-16 03:23:58,167] [INFO] Query marker FASTA was written to OceanDNA-b24739/markers.fasta
[2023-03-16 03:23:58,168] [INFO] Task started: Blastn
[2023-03-16 03:23:58,168] [INFO] Running command: blastn -query OceanDNA-b24739/markers.fasta -db /var/lib/cwl/stg9c4355fe-1177-48bc-b394-6fc136ee767f/dqc_reference/reference_markers.fasta -out OceanDNA-b24739/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:23:58,706] [INFO] Task succeeded: Blastn
[2023-03-16 03:23:58,707] [INFO] Selected 22 target genomes.
[2023-03-16 03:23:58,707] [INFO] Target genome list was writen to OceanDNA-b24739/target_genomes.txt
[2023-03-16 03:23:58,717] [INFO] Task started: fastANI
[2023-03-16 03:23:58,717] [INFO] Running command: fastANI --query /var/lib/cwl/stge4fc5534-2368-4a13-9a45-3da246f2684f/OceanDNA-b24739.fa --refList OceanDNA-b24739/target_genomes.txt --output OceanDNA-b24739/fastani_result.tsv --threads 1
[2023-03-16 03:24:07,928] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:07,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c4355fe-1177-48bc-b394-6fc136ee767f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:07,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c4355fe-1177-48bc-b394-6fc136ee767f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:07,929] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:07,929] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:07,929] [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 03:24:07,929] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24739/tc_result.tsv
[2023-03-16 03:24:07,929] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:07,929] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:07,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c4355fe-1177-48bc-b394-6fc136ee767f/dqc_reference/checkm_data
[2023-03-16 03:24:07,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:07,936] [INFO] Task started: CheckM
[2023-03-16 03:24:07,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24739/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24739/checkm_input OceanDNA-b24739/checkm_result
[2023-03-16 03:24:34,340] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:34,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.48%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:34,343] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:34,343] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:34,343] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24739/markers.fasta)
[2023-03-16 03:24:34,343] [INFO] Task started: Blastn
[2023-03-16 03:24:34,343] [INFO] Running command: blastn -query OceanDNA-b24739/markers.fasta -db /var/lib/cwl/stg9c4355fe-1177-48bc-b394-6fc136ee767f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24739/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:35,166] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:35,167] [INFO] Selected 10 target genomes.
[2023-03-16 03:24:35,167] [INFO] Target genome list was writen to OceanDNA-b24739/target_genomes_gtdb.txt
[2023-03-16 03:24:35,436] [INFO] Task started: fastANI
[2023-03-16 03:24:35,436] [INFO] Running command: fastANI --query /var/lib/cwl/stge4fc5534-2368-4a13-9a45-3da246f2684f/OceanDNA-b24739.fa --refList OceanDNA-b24739/target_genomes_gtdb.txt --output OceanDNA-b24739/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:39,592] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:39,596] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:24:39,596] [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_902589475.1	s__GCA-002701455 sp902589475	94.0847	297	482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690995.1	s__GCA-002701455 sp002690995	93.8949	425	482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	95.85	95.85	0.80	0.80	2	-
GCA_902578675.1	s__GCA-002701455 sp902578675	93.2468	241	482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	97.96	97.96	0.68	0.68	2	-
GCA_002730675.1	s__GCA-002701455 sp002730675	89.379	308	482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902629125.1	s__GCA-002701455 sp902629125	88.3963	330	482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	98.54	98.54	0.68	0.68	2	-
GCA_002701455.1	s__GCA-002701455 sp002701455	78.1467	191	482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	98.37	98.37	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:39,597] [INFO] GTDB search result was written to OceanDNA-b24739/result_gtdb.tsv
[2023-03-16 03:24:39,597] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:39,597] [INFO] DFAST_QC result json was written to OceanDNA-b24739/dqc_result.json
[2023-03-16 03:24:39,598] [INFO] DFAST_QC completed!
[2023-03-16 03:24:39,598] [INFO] Total running time: 0h0m52s