[2023-03-15 04:45:50,554] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:50,556] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:50,556] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcf45050-24d4-4e49-a1d0-e11b94eee176/dqc_reference
[2023-03-15 04:45:51,670] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:51,670] [INFO] Task started: Prodigal
[2023-03-15 04:45:51,670] [INFO] Running command: cat /var/lib/cwl/stgb1442b32-1dce-4e55-947a-e9794fbdcb41/OceanDNA-b21259.fa | prodigal -d OceanDNA-b21259/cds.fna -a OceanDNA-b21259/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:45:55,047] [INFO] Task succeeded: Prodigal
[2023-03-15 04:45:55,047] [INFO] Task started: HMMsearch
[2023-03-15 04:45:55,047] [INFO] Running command: hmmsearch --tblout OceanDNA-b21259/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcf45050-24d4-4e49-a1d0-e11b94eee176/dqc_reference/reference_markers.hmm OceanDNA-b21259/protein.faa > /dev/null
[2023-03-15 04:45:55,215] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:45:55,215] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb1442b32-1dce-4e55-947a-e9794fbdcb41/OceanDNA-b21259.fa]
[2023-03-15 04:45:55,250] [INFO] Query marker FASTA was written to OceanDNA-b21259/markers.fasta
[2023-03-15 04:45:55,251] [INFO] Task started: Blastn
[2023-03-15 04:45:55,251] [INFO] Running command: blastn -query OceanDNA-b21259/markers.fasta -db /var/lib/cwl/stgdcf45050-24d4-4e49-a1d0-e11b94eee176/dqc_reference/reference_markers.fasta -out OceanDNA-b21259/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:45:55,754] [INFO] Task succeeded: Blastn
[2023-03-15 04:45:55,760] [INFO] Selected 10 target genomes.
[2023-03-15 04:45:55,760] [INFO] Target genome list was writen to OceanDNA-b21259/target_genomes.txt
[2023-03-15 04:45:55,766] [INFO] Task started: fastANI
[2023-03-15 04:45:55,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1442b32-1dce-4e55-947a-e9794fbdcb41/OceanDNA-b21259.fa --refList OceanDNA-b21259/target_genomes.txt --output OceanDNA-b21259/fastani_result.tsv --threads 1
[2023-03-15 04:45:59,810] [INFO] Task succeeded: fastANI
[2023-03-15 04:45:59,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcf45050-24d4-4e49-a1d0-e11b94eee176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:45:59,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcf45050-24d4-4e49-a1d0-e11b94eee176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:45:59,810] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:45:59,810] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:45:59,811] [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 04:45:59,813] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21259/tc_result.tsv
[2023-03-15 04:45:59,818] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:45:59,818] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:45:59,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcf45050-24d4-4e49-a1d0-e11b94eee176/dqc_reference/checkm_data
[2023-03-15 04:45:59,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:45:59,827] [INFO] Task started: CheckM
[2023-03-15 04:45:59,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21259/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21259/checkm_input OceanDNA-b21259/checkm_result
[2023-03-15 04:46:14,906] [INFO] Task succeeded: CheckM
[2023-03-15 04:46:14,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:46:14,946] [INFO] ===== Completeness check finished =====
[2023-03-15 04:46:14,946] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:46:14,946] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21259/markers.fasta)
[2023-03-15 04:46:14,947] [INFO] Task started: Blastn
[2023-03-15 04:46:14,947] [INFO] Running command: blastn -query OceanDNA-b21259/markers.fasta -db /var/lib/cwl/stgdcf45050-24d4-4e49-a1d0-e11b94eee176/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21259/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:15,688] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:15,694] [INFO] Selected 14 target genomes.
[2023-03-15 04:46:15,694] [INFO] Target genome list was writen to OceanDNA-b21259/target_genomes_gtdb.txt
[2023-03-15 04:46:15,711] [INFO] Task started: fastANI
[2023-03-15 04:46:15,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1442b32-1dce-4e55-947a-e9794fbdcb41/OceanDNA-b21259.fa --refList OceanDNA-b21259/target_genomes_gtdb.txt --output OceanDNA-b21259/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:46:20,479] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:20,482] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:46:20,482] [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_000372225.1	s__Nitromaritima sp000372225	92.9409	106	137	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647025.1	s__Nitromaritima sp018647025	82.1372	85	137	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	98.38	98.13	0.71	0.67	3	-
GCA_018697205.1	s__Nitromaritima sp018697205	80.8817	116	137	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	99.64	99.64	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:46:20,485] [INFO] GTDB search result was written to OceanDNA-b21259/result_gtdb.tsv
[2023-03-15 04:46:20,485] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:46:20,487] [INFO] DFAST_QC result json was written to OceanDNA-b21259/dqc_result.json
[2023-03-15 04:46:20,487] [INFO] DFAST_QC completed!
[2023-03-15 04:46:20,487] [INFO] Total running time: 0h0m30s