[2023-03-18 02:27:59,044] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:59,044] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:59,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg812af2c7-dafa-4703-9791-afd1ce8f84d3/dqc_reference
[2023-03-18 02:28:00,176] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:28:00,177] [INFO] Task started: Prodigal
[2023-03-18 02:28:00,177] [INFO] Running command: cat /var/lib/cwl/stg11db2be2-c66b-4885-9dd2-758258e46d6f/OceanDNA-b21284.fa | prodigal -d OceanDNA-b21284/cds.fna -a OceanDNA-b21284/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:06,359] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:06,359] [INFO] Task started: HMMsearch
[2023-03-18 02:28:06,359] [INFO] Running command: hmmsearch --tblout OceanDNA-b21284/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg812af2c7-dafa-4703-9791-afd1ce8f84d3/dqc_reference/reference_markers.hmm OceanDNA-b21284/protein.faa > /dev/null
[2023-03-18 02:28:06,507] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:06,508] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg11db2be2-c66b-4885-9dd2-758258e46d6f/OceanDNA-b21284.fa]
[2023-03-18 02:28:06,519] [INFO] Query marker FASTA was written to OceanDNA-b21284/markers.fasta
[2023-03-18 02:28:06,520] [INFO] Task started: Blastn
[2023-03-18 02:28:06,520] [INFO] Running command: blastn -query OceanDNA-b21284/markers.fasta -db /var/lib/cwl/stg812af2c7-dafa-4703-9791-afd1ce8f84d3/dqc_reference/reference_markers.fasta -out OceanDNA-b21284/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:07,018] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:07,019] [INFO] Selected 16 target genomes.
[2023-03-18 02:28:07,019] [INFO] Target genome list was writen to OceanDNA-b21284/target_genomes.txt
[2023-03-18 02:28:07,028] [INFO] Task started: fastANI
[2023-03-18 02:28:07,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg11db2be2-c66b-4885-9dd2-758258e46d6f/OceanDNA-b21284.fa --refList OceanDNA-b21284/target_genomes.txt --output OceanDNA-b21284/fastani_result.tsv --threads 1
[2023-03-18 02:28:15,094] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:15,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg812af2c7-dafa-4703-9791-afd1ce8f84d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:15,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg812af2c7-dafa-4703-9791-afd1ce8f84d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:15,095] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:15,095] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:28:15,095] [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
--------------------------------------------------------------------------------
[2023-03-18 02:28:15,095] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21284/tc_result.tsv
[2023-03-18 02:28:15,096] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:15,096] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:15,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg812af2c7-dafa-4703-9791-afd1ce8f84d3/dqc_reference/checkm_data
[2023-03-18 02:28:15,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:15,102] [INFO] Task started: CheckM
[2023-03-18 02:28:15,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21284/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21284/checkm_input OceanDNA-b21284/checkm_result
[2023-03-18 02:28:36,205] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:36,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.55%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:36,207] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:36,208] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:36,208] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21284/markers.fasta)
[2023-03-18 02:28:36,208] [INFO] Task started: Blastn
[2023-03-18 02:28:36,208] [INFO] Running command: blastn -query OceanDNA-b21284/markers.fasta -db /var/lib/cwl/stg812af2c7-dafa-4703-9791-afd1ce8f84d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21284/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:36,865] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:36,866] [INFO] Selected 17 target genomes.
[2023-03-18 02:28:36,866] [INFO] Target genome list was writen to OceanDNA-b21284/target_genomes_gtdb.txt
[2023-03-18 02:28:36,885] [INFO] Task started: fastANI
[2023-03-18 02:28:36,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg11db2be2-c66b-4885-9dd2-758258e46d6f/OceanDNA-b21284.fa --refList OceanDNA-b21284/target_genomes_gtdb.txt --output OceanDNA-b21284/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:42,587] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:42,591] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:28:42,591] [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	90.0869	226	340	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	80.5595	181	340	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	79.6308	213	340	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	99.64	99.64	0.83	0.83	2	-
GCA_905182935.1	s__Nitromaritima sp905182935	77.0584	88	340	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:28:42,591] [INFO] GTDB search result was written to OceanDNA-b21284/result_gtdb.tsv
[2023-03-18 02:28:42,591] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:42,592] [INFO] DFAST_QC result json was written to OceanDNA-b21284/dqc_result.json
[2023-03-18 02:28:42,592] [INFO] DFAST_QC completed!
[2023-03-18 02:28:42,592] [INFO] Total running time: 0h0m44s