[2023-03-16 04:54:07,041] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,042] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4f229c7-d907-48a4-a0d6-c749db35ecb2/dqc_reference
[2023-03-16 04:54:08,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,358] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,358] [INFO] Running command: cat /var/lib/cwl/stg9e7b1871-244d-4725-bf02-60e122292447/OceanDNA-b21016.fa | prodigal -d OceanDNA-b21016/cds.fna -a OceanDNA-b21016/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:26,009] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:26,009] [INFO] Task started: HMMsearch
[2023-03-16 04:54:26,009] [INFO] Running command: hmmsearch --tblout OceanDNA-b21016/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4f229c7-d907-48a4-a0d6-c749db35ecb2/dqc_reference/reference_markers.hmm OceanDNA-b21016/protein.faa > /dev/null
[2023-03-16 04:54:26,276] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:26,276] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9e7b1871-244d-4725-bf02-60e122292447/OceanDNA-b21016.fa]
[2023-03-16 04:54:26,305] [INFO] Query marker FASTA was written to OceanDNA-b21016/markers.fasta
[2023-03-16 04:54:26,306] [INFO] Task started: Blastn
[2023-03-16 04:54:26,306] [INFO] Running command: blastn -query OceanDNA-b21016/markers.fasta -db /var/lib/cwl/stgb4f229c7-d907-48a4-a0d6-c749db35ecb2/dqc_reference/reference_markers.fasta -out OceanDNA-b21016/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:26,899] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:26,900] [INFO] Selected 25 target genomes.
[2023-03-16 04:54:26,900] [INFO] Target genome list was writen to OceanDNA-b21016/target_genomes.txt
[2023-03-16 04:54:26,915] [INFO] Task started: fastANI
[2023-03-16 04:54:26,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e7b1871-244d-4725-bf02-60e122292447/OceanDNA-b21016.fa --refList OceanDNA-b21016/target_genomes.txt --output OceanDNA-b21016/fastani_result.tsv --threads 1
[2023-03-16 04:54:46,000] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:46,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4f229c7-d907-48a4-a0d6-c749db35ecb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:46,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4f229c7-d907-48a4-a0d6-c749db35ecb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:46,001] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:46,001] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:46,001] [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 04:54:46,002] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21016/tc_result.tsv
[2023-03-16 04:54:46,002] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:46,002] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:46,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4f229c7-d907-48a4-a0d6-c749db35ecb2/dqc_reference/checkm_data
[2023-03-16 04:54:46,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:46,122] [INFO] Task started: CheckM
[2023-03-16 04:54:46,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21016/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21016/checkm_input OceanDNA-b21016/checkm_result
[2023-03-16 04:55:31,580] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:31,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:31,583] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:31,583] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:31,584] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21016/markers.fasta)
[2023-03-16 04:55:31,584] [INFO] Task started: Blastn
[2023-03-16 04:55:31,584] [INFO] Running command: blastn -query OceanDNA-b21016/markers.fasta -db /var/lib/cwl/stgb4f229c7-d907-48a4-a0d6-c749db35ecb2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21016/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:32,444] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:32,444] [INFO] Selected 15 target genomes.
[2023-03-16 04:55:32,444] [INFO] Target genome list was writen to OceanDNA-b21016/target_genomes_gtdb.txt
[2023-03-16 04:55:32,464] [INFO] Task started: fastANI
[2023-03-16 04:55:32,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e7b1871-244d-4725-bf02-60e122292447/OceanDNA-b21016.fa --refList OceanDNA-b21016/target_genomes_gtdb.txt --output OceanDNA-b21016/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:43,898] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:43,903] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:55:43,903] [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_012959665.1	s__JAZXM01 sp012959665	93.4209	696	910	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JAZXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959865.1	s__JAZXM01 sp012959865	81.7843	467	910	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JAZXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240165.1	s__JAZXM01 sp014240165	77.708	287	910	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JAZXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691025.1	s__MED660 sp002691025	75.9968	61	910	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__MED660	95.0	100.00	100.00	0.97	0.97	2	-
GCA_002691205.1	s__MED660 sp002691205	75.763	54	910	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__MED660	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	75.1918	58	910	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:43,903] [INFO] GTDB search result was written to OceanDNA-b21016/result_gtdb.tsv
[2023-03-16 04:55:43,903] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:43,904] [INFO] DFAST_QC result json was written to OceanDNA-b21016/dqc_result.json
[2023-03-16 04:55:43,904] [INFO] DFAST_QC completed!
[2023-03-16 04:55:43,904] [INFO] Total running time: 0h1m37s