[2023-03-16 04:05:20,415] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,415] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg79f84972-3fd1-4902-8dfa-883242fa3dee/dqc_reference
[2023-03-16 04:05:22,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,127] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,127] [INFO] Running command: cat /var/lib/cwl/stg24b9cd7b-dc9e-4d22-a780-aee2134e7ddf/OceanDNA-b10437.fa | prodigal -d OceanDNA-b10437/cds.fna -a OceanDNA-b10437/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:29,671] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:29,671] [INFO] Task started: HMMsearch
[2023-03-16 04:05:29,671] [INFO] Running command: hmmsearch --tblout OceanDNA-b10437/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79f84972-3fd1-4902-8dfa-883242fa3dee/dqc_reference/reference_markers.hmm OceanDNA-b10437/protein.faa > /dev/null
[2023-03-16 04:05:29,823] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:29,823] [INFO] Found 6/6 markers.
[2023-03-16 04:05:29,834] [INFO] Query marker FASTA was written to OceanDNA-b10437/markers.fasta
[2023-03-16 04:05:29,834] [INFO] Task started: Blastn
[2023-03-16 04:05:29,834] [INFO] Running command: blastn -query OceanDNA-b10437/markers.fasta -db /var/lib/cwl/stg79f84972-3fd1-4902-8dfa-883242fa3dee/dqc_reference/reference_markers.fasta -out OceanDNA-b10437/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:30,414] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:30,414] [INFO] Selected 26 target genomes.
[2023-03-16 04:05:30,415] [INFO] Target genome list was writen to OceanDNA-b10437/target_genomes.txt
[2023-03-16 04:05:30,426] [INFO] Task started: fastANI
[2023-03-16 04:05:30,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg24b9cd7b-dc9e-4d22-a780-aee2134e7ddf/OceanDNA-b10437.fa --refList OceanDNA-b10437/target_genomes.txt --output OceanDNA-b10437/fastani_result.tsv --threads 1
[2023-03-16 04:05:43,571] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:43,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79f84972-3fd1-4902-8dfa-883242fa3dee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:43,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79f84972-3fd1-4902-8dfa-883242fa3dee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:43,572] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:43,572] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:05:43,572] [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 04:05:43,572] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10437/tc_result.tsv
[2023-03-16 04:05:43,572] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:43,572] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:43,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79f84972-3fd1-4902-8dfa-883242fa3dee/dqc_reference/checkm_data
[2023-03-16 04:05:43,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:43,579] [INFO] Task started: CheckM
[2023-03-16 04:05:43,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10437/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10437/checkm_input OceanDNA-b10437/checkm_result
[2023-03-16 04:06:07,439] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:07,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:07,441] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:07,441] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:07,441] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10437/markers.fasta)
[2023-03-16 04:06:07,441] [INFO] Task started: Blastn
[2023-03-16 04:06:07,441] [INFO] Running command: blastn -query OceanDNA-b10437/markers.fasta -db /var/lib/cwl/stg79f84972-3fd1-4902-8dfa-883242fa3dee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10437/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:08,380] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:08,381] [INFO] Selected 23 target genomes.
[2023-03-16 04:06:08,381] [INFO] Target genome list was writen to OceanDNA-b10437/target_genomes_gtdb.txt
[2023-03-16 04:06:08,431] [INFO] Task started: fastANI
[2023-03-16 04:06:08,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg24b9cd7b-dc9e-4d22-a780-aee2134e7ddf/OceanDNA-b10437.fa --refList OceanDNA-b10437/target_genomes_gtdb.txt --output OceanDNA-b10437/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:15,252] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:15,257] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:06:15,257] [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_002702875.1	s__TMED220 sp002702875	98.0834	344	424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905381055.1	s__TMED220 sp905381055	76.6236	125	424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169155.2	s__TMED220 sp002169155	76.2664	68	424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	76.2351	50	424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_902598305.1	s__TMED96 sp902598305	75.5968	56	424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713495.1	s__GCA-002723295 sp002713495	75.5551	50	424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:15,257] [INFO] GTDB search result was written to OceanDNA-b10437/result_gtdb.tsv
[2023-03-16 04:06:15,257] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:15,258] [INFO] DFAST_QC result json was written to OceanDNA-b10437/dqc_result.json
[2023-03-16 04:06:15,258] [INFO] DFAST_QC completed!
[2023-03-16 04:06:15,258] [INFO] Total running time: 0h0m55s