[2023-03-18 10:46:22,265] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:46:22,265] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:46:22,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d662440-0e6d-429d-97d9-f9656d7cee2e/dqc_reference
[2023-03-18 10:46:23,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:46:23,349] [INFO] Task started: Prodigal
[2023-03-18 10:46:23,349] [INFO] Running command: cat /var/lib/cwl/stg1ffe2b3c-2e74-4078-84f0-3923d2c80cb4/OceanDNA-b334.fa | prodigal -d OceanDNA-b334/cds.fna -a OceanDNA-b334/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:46:28,085] [INFO] Task succeeded: Prodigal
[2023-03-18 10:46:28,085] [INFO] Task started: HMMsearch
[2023-03-18 10:46:28,085] [INFO] Running command: hmmsearch --tblout OceanDNA-b334/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d662440-0e6d-429d-97d9-f9656d7cee2e/dqc_reference/reference_markers.hmm OceanDNA-b334/protein.faa > /dev/null
[2023-03-18 10:46:28,256] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:46:28,257] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1ffe2b3c-2e74-4078-84f0-3923d2c80cb4/OceanDNA-b334.fa]
[2023-03-18 10:46:28,265] [INFO] Query marker FASTA was written to OceanDNA-b334/markers.fasta
[2023-03-18 10:46:28,266] [INFO] Task started: Blastn
[2023-03-18 10:46:28,266] [INFO] Running command: blastn -query OceanDNA-b334/markers.fasta -db /var/lib/cwl/stg0d662440-0e6d-429d-97d9-f9656d7cee2e/dqc_reference/reference_markers.fasta -out OceanDNA-b334/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:46:28,958] [INFO] Task succeeded: Blastn
[2023-03-18 10:46:28,960] [INFO] Selected 12 target genomes.
[2023-03-18 10:46:28,960] [INFO] Target genome list was writen to OceanDNA-b334/target_genomes.txt
[2023-03-18 10:46:28,967] [INFO] Task started: fastANI
[2023-03-18 10:46:28,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ffe2b3c-2e74-4078-84f0-3923d2c80cb4/OceanDNA-b334.fa --refList OceanDNA-b334/target_genomes.txt --output OceanDNA-b334/fastani_result.tsv --threads 1
[2023-03-18 10:46:36,993] [INFO] Task succeeded: fastANI
[2023-03-18 10:46:36,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d662440-0e6d-429d-97d9-f9656d7cee2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:46:36,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d662440-0e6d-429d-97d9-f9656d7cee2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:46:36,994] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:46:36,994] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:46:36,994] [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 10:46:36,994] [INFO] DFAST Taxonomy check result was written to OceanDNA-b334/tc_result.tsv
[2023-03-18 10:46:36,995] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:46:36,995] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:46:36,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d662440-0e6d-429d-97d9-f9656d7cee2e/dqc_reference/checkm_data
[2023-03-18 10:46:36,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:46:37,026] [INFO] Task started: CheckM
[2023-03-18 10:46:37,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b334/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b334/checkm_input OceanDNA-b334/checkm_result
[2023-03-18 10:46:55,464] [INFO] Task succeeded: CheckM
[2023-03-18 10:46:55,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:46:55,486] [INFO] ===== Completeness check finished =====
[2023-03-18 10:46:55,486] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:46:55,486] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b334/markers.fasta)
[2023-03-18 10:46:55,486] [INFO] Task started: Blastn
[2023-03-18 10:46:55,486] [INFO] Running command: blastn -query OceanDNA-b334/markers.fasta -db /var/lib/cwl/stg0d662440-0e6d-429d-97d9-f9656d7cee2e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b334/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:46:56,384] [INFO] Task succeeded: Blastn
[2023-03-18 10:46:56,385] [INFO] Selected 10 target genomes.
[2023-03-18 10:46:56,385] [INFO] Target genome list was writen to OceanDNA-b334/target_genomes_gtdb.txt
[2023-03-18 10:46:56,395] [INFO] Task started: fastANI
[2023-03-18 10:46:56,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ffe2b3c-2e74-4078-84f0-3923d2c80cb4/OceanDNA-b334.fa --refList OceanDNA-b334/target_genomes_gtdb.txt --output OceanDNA-b334/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:46:58,921] [INFO] Task succeeded: fastANI
[2023-03-18 10:46:58,926] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:46:58,926] [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_005800965.1	s__F1-60-MAGs027 sp005800965	91.8663	143	192	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463775.1	s__F1-60-MAGs027 sp016463775	81.9074	137	192	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870295.1	s__F1-60-MAGs027 sp016870295	78.5609	63	192	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005793785.1	s__F1-60-MAGs027 sp005793785	78.3491	63	192	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	98.94	98.60	0.81	0.74	4	-
GCA_005793215.1	s__F1-60-MAGs027 sp005793215	78.3475	82	192	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	98.97	98.30	0.86	0.85	4	-
GCA_009927665.1	s__F1-60-MAGs027 sp009927665	78.1238	74	192	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	99.21	99.09	0.94	0.94	3	-
GCA_017856115.1	s__F1-60-MAGs027 sp017856115	78.117	97	192	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853375.1	s__F1-60-MAGs027 sp017853375	77.8785	93	192	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:46:58,927] [INFO] GTDB search result was written to OceanDNA-b334/result_gtdb.tsv
[2023-03-18 10:46:58,928] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:46:58,929] [INFO] DFAST_QC result json was written to OceanDNA-b334/dqc_result.json
[2023-03-18 10:46:58,929] [INFO] DFAST_QC completed!
[2023-03-18 10:46:58,929] [INFO] Total running time: 0h0m37s