[2023-03-15 11:24:11,505] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:24:11,505] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:24:11,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg9094df93-9f85-44c1-af35-dd0b87e20041/dqc_reference
[2023-03-15 11:24:12,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:24:12,608] [INFO] Task started: Prodigal
[2023-03-15 11:24:12,609] [INFO] Running command: cat /var/lib/cwl/stgfc571656-7e3f-45f6-a752-ac07ce135d51/OceanDNA-b11993.fa | prodigal -d OceanDNA-b11993/cds.fna -a OceanDNA-b11993/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:24:37,121] [INFO] Task succeeded: Prodigal
[2023-03-15 11:24:37,121] [INFO] Task started: HMMsearch
[2023-03-15 11:24:37,121] [INFO] Running command: hmmsearch --tblout OceanDNA-b11993/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9094df93-9f85-44c1-af35-dd0b87e20041/dqc_reference/reference_markers.hmm OceanDNA-b11993/protein.faa > /dev/null
[2023-03-15 11:24:37,291] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:24:37,292] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfc571656-7e3f-45f6-a752-ac07ce135d51/OceanDNA-b11993.fa]
[2023-03-15 11:24:37,308] [INFO] Query marker FASTA was written to OceanDNA-b11993/markers.fasta
[2023-03-15 11:24:37,308] [INFO] Task started: Blastn
[2023-03-15 11:24:37,308] [INFO] Running command: blastn -query OceanDNA-b11993/markers.fasta -db /var/lib/cwl/stg9094df93-9f85-44c1-af35-dd0b87e20041/dqc_reference/reference_markers.fasta -out OceanDNA-b11993/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:37,841] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:37,842] [INFO] Selected 22 target genomes.
[2023-03-15 11:24:37,842] [INFO] Target genome list was writen to OceanDNA-b11993/target_genomes.txt
[2023-03-15 11:24:37,854] [INFO] Task started: fastANI
[2023-03-15 11:24:37,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc571656-7e3f-45f6-a752-ac07ce135d51/OceanDNA-b11993.fa --refList OceanDNA-b11993/target_genomes.txt --output OceanDNA-b11993/fastani_result.tsv --threads 1
[2023-03-15 11:24:51,263] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:51,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9094df93-9f85-44c1-af35-dd0b87e20041/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:24:51,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9094df93-9f85-44c1-af35-dd0b87e20041/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:24:51,264] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:24:51,264] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:24:51,264] [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 11:24:51,373] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11993/tc_result.tsv
[2023-03-15 11:24:51,373] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:24:51,374] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:24:51,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9094df93-9f85-44c1-af35-dd0b87e20041/dqc_reference/checkm_data
[2023-03-15 11:24:51,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:24:51,407] [INFO] Task started: CheckM
[2023-03-15 11:24:51,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11993/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11993/checkm_input OceanDNA-b11993/checkm_result
[2023-03-15 11:25:55,920] [INFO] Task succeeded: CheckM
[2023-03-15 11:25:55,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.13%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:25:55,926] [INFO] ===== Completeness check finished =====
[2023-03-15 11:25:55,926] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:25:55,926] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11993/markers.fasta)
[2023-03-15 11:25:55,928] [INFO] Task started: Blastn
[2023-03-15 11:25:55,928] [INFO] Running command: blastn -query OceanDNA-b11993/markers.fasta -db /var/lib/cwl/stg9094df93-9f85-44c1-af35-dd0b87e20041/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11993/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:25:56,650] [INFO] Task succeeded: Blastn
[2023-03-15 11:25:56,651] [INFO] Selected 21 target genomes.
[2023-03-15 11:25:56,651] [INFO] Target genome list was writen to OceanDNA-b11993/target_genomes_gtdb.txt
[2023-03-15 11:25:56,696] [INFO] Task started: fastANI
[2023-03-15 11:25:56,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc571656-7e3f-45f6-a752-ac07ce135d51/OceanDNA-b11993.fa --refList OceanDNA-b11993/target_genomes_gtdb.txt --output OceanDNA-b11993/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:26:07,259] [INFO] Task succeeded: fastANI
[2023-03-15 11:26:07,264] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:26:07,264] [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_002336475.1	s__UBA8752 sp002336475	99.5981	681	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.51	99.51	0.88	0.88	2	conclusive
GCA_905478795.1	s__UBA8752 sp905478795	80.5547	494	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780385.1	s__UBA8752 sp016780385	79.676	276	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389295.1	s__UBA8752 sp002389295	78.8421	310	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.36	99.34	0.83	0.82	3	-
GCA_002172485.2	s__UBA8752 sp002172485	77.9717	154	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862785.1	s__UBA8752 sp002862785	77.7543	237	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902535565.1	s__UBA8752 sp902535565	77.3929	78	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522855.1	s__UBA8752 sp011522855	77.3195	153	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:26:07,265] [INFO] GTDB search result was written to OceanDNA-b11993/result_gtdb.tsv
[2023-03-15 11:26:07,266] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:26:07,268] [INFO] DFAST_QC result json was written to OceanDNA-b11993/dqc_result.json
[2023-03-15 11:26:07,268] [INFO] DFAST_QC completed!
[2023-03-15 11:26:07,268] [INFO] Total running time: 0h1m56s