[2023-03-15 23:07:02,638] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,638] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg478f16d7-26b1-4281-aa17-e759617db2c7/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,967] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,967] [INFO] Running command: cat /var/lib/cwl/stg2a35e518-325e-483e-9b73-cf3837070256/OceanDNA-b8791.fa | prodigal -d OceanDNA-b8791/cds.fna -a OceanDNA-b8791/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:07,831] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:07,831] [INFO] Task started: HMMsearch
[2023-03-15 23:07:07,831] [INFO] Running command: hmmsearch --tblout OceanDNA-b8791/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg478f16d7-26b1-4281-aa17-e759617db2c7/dqc_reference/reference_markers.hmm OceanDNA-b8791/protein.faa > /dev/null
[2023-03-15 23:07:07,982] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:07,983] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2a35e518-325e-483e-9b73-cf3837070256/OceanDNA-b8791.fa]
[2023-03-15 23:07:07,991] [INFO] Query marker FASTA was written to OceanDNA-b8791/markers.fasta
[2023-03-15 23:07:07,992] [INFO] Task started: Blastn
[2023-03-15 23:07:07,992] [INFO] Running command: blastn -query OceanDNA-b8791/markers.fasta -db /var/lib/cwl/stg478f16d7-26b1-4281-aa17-e759617db2c7/dqc_reference/reference_markers.fasta -out OceanDNA-b8791/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:08,487] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:08,488] [INFO] Selected 22 target genomes.
[2023-03-15 23:07:08,488] [INFO] Target genome list was writen to OceanDNA-b8791/target_genomes.txt
[2023-03-15 23:07:08,555] [INFO] Task started: fastANI
[2023-03-15 23:07:08,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a35e518-325e-483e-9b73-cf3837070256/OceanDNA-b8791.fa --refList OceanDNA-b8791/target_genomes.txt --output OceanDNA-b8791/fastani_result.tsv --threads 1
[2023-03-15 23:07:19,773] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:19,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg478f16d7-26b1-4281-aa17-e759617db2c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:19,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg478f16d7-26b1-4281-aa17-e759617db2c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:19,773] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:19,773] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:07:19,773] [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 23:07:19,774] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8791/tc_result.tsv
[2023-03-15 23:07:19,774] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:19,774] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:19,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg478f16d7-26b1-4281-aa17-e759617db2c7/dqc_reference/checkm_data
[2023-03-15 23:07:19,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:19,785] [INFO] Task started: CheckM
[2023-03-15 23:07:19,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8791/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8791/checkm_input OceanDNA-b8791/checkm_result
[2023-03-15 23:07:36,126] [INFO] Task succeeded: CheckM
[2023-03-15 23:07:36,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:07:36,127] [INFO] ===== Completeness check finished =====
[2023-03-15 23:07:36,128] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:07:36,128] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8791/markers.fasta)
[2023-03-15 23:07:36,128] [INFO] Task started: Blastn
[2023-03-15 23:07:36,128] [INFO] Running command: blastn -query OceanDNA-b8791/markers.fasta -db /var/lib/cwl/stg478f16d7-26b1-4281-aa17-e759617db2c7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8791/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:36,786] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:36,787] [INFO] Selected 11 target genomes.
[2023-03-15 23:07:36,787] [INFO] Target genome list was writen to OceanDNA-b8791/target_genomes_gtdb.txt
[2023-03-15 23:07:36,819] [INFO] Task started: fastANI
[2023-03-15 23:07:36,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a35e518-325e-483e-9b73-cf3837070256/OceanDNA-b8791.fa --refList OceanDNA-b8791/target_genomes_gtdb.txt --output OceanDNA-b8791/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:07:39,050] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:39,055] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-15 23:07:39,055] [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_902535165.1	s__MED-G14 sp902535165	98.3384	168	198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902546095.1	s__MED-G14 sp902546095	95.0302	136	198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902597545.1	s__MED-G14 sp902597545	93.2391	179	198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.96	95.61	0.87	0.83	5	-
GCA_902610105.1	s__MED-G14 sp902610105	88.8331	105	198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606555.1	s__MED-G14 sp902606555	88.5308	116	198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331885.1	s__MED-G14 sp003331885	78.7707	99	198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.85	96.85	0.80	0.80	2	-
GCA_902587325.1	s__MED-G14 sp902587325	77.3009	61	198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.53	95.17	0.82	0.78	10	-
--------------------------------------------------------------------------------
[2023-03-15 23:07:39,055] [INFO] GTDB search result was written to OceanDNA-b8791/result_gtdb.tsv
[2023-03-15 23:07:39,055] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:07:39,056] [INFO] DFAST_QC result json was written to OceanDNA-b8791/dqc_result.json
[2023-03-15 23:07:39,056] [INFO] DFAST_QC completed!
[2023-03-15 23:07:39,056] [INFO] Total running time: 0h0m36s