[2023-03-14 15:01:55,967] [INFO] DFAST_QC pipeline started.
[2023-03-14 15:01:55,967] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 15:01:55,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a1436cf-cdae-4688-8240-cc410189caef/dqc_reference
[2023-03-14 15:01:59,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 15:01:59,389] [INFO] Task started: Prodigal
[2023-03-14 15:01:59,389] [INFO] Running command: cat /var/lib/cwl/stg8a9ed0f8-3b87-4d74-80fe-362d7df24a19/OceanDNA-b41825.fa | prodigal -d OceanDNA-b41825/cds.fna -a OceanDNA-b41825/protein.faa -g 11 -q > /dev/null
[2023-03-14 15:02:04,866] [INFO] Task succeeded: Prodigal
[2023-03-14 15:02:04,867] [INFO] Task started: HMMsearch
[2023-03-14 15:02:04,867] [INFO] Running command: hmmsearch --tblout OceanDNA-b41825/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a1436cf-cdae-4688-8240-cc410189caef/dqc_reference/reference_markers.hmm OceanDNA-b41825/protein.faa > /dev/null
[2023-03-14 15:02:05,049] [INFO] Task succeeded: HMMsearch
[2023-03-14 15:02:05,049] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8a9ed0f8-3b87-4d74-80fe-362d7df24a19/OceanDNA-b41825.fa]
[2023-03-14 15:02:05,058] [INFO] Query marker FASTA was written to OceanDNA-b41825/markers.fasta
[2023-03-14 15:02:05,059] [INFO] Task started: Blastn
[2023-03-14 15:02:05,059] [INFO] Running command: blastn -query OceanDNA-b41825/markers.fasta -db /var/lib/cwl/stg2a1436cf-cdae-4688-8240-cc410189caef/dqc_reference/reference_markers.fasta -out OceanDNA-b41825/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:02:09,020] [INFO] Task succeeded: Blastn
[2023-03-14 15:02:09,021] [INFO] Selected 15 target genomes.
[2023-03-14 15:02:09,021] [INFO] Target genome list was writen to OceanDNA-b41825/target_genomes.txt
[2023-03-14 15:02:09,035] [INFO] Task started: fastANI
[2023-03-14 15:02:09,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a9ed0f8-3b87-4d74-80fe-362d7df24a19/OceanDNA-b41825.fa --refList OceanDNA-b41825/target_genomes.txt --output OceanDNA-b41825/fastani_result.tsv --threads 1
[2023-03-14 15:02:21,732] [INFO] Task succeeded: fastANI
[2023-03-14 15:02:21,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a1436cf-cdae-4688-8240-cc410189caef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 15:02:21,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a1436cf-cdae-4688-8240-cc410189caef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 15:02:21,733] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 15:02:21,733] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 15:02:21,733] [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
--------------------------------------------------------------------------------
[2023-03-14 15:02:21,733] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41825/tc_result.tsv
[2023-03-14 15:02:21,734] [INFO] ===== Taxonomy check completed =====
[2023-03-14 15:02:21,734] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 15:02:21,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a1436cf-cdae-4688-8240-cc410189caef/dqc_reference/checkm_data
[2023-03-14 15:02:21,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 15:02:21,790] [INFO] Task started: CheckM
[2023-03-14 15:02:21,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41825/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41825/checkm_input OceanDNA-b41825/checkm_result
[2023-03-14 15:02:42,548] [INFO] Task succeeded: CheckM
[2023-03-14 15:02:42,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.34%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 15:02:42,550] [INFO] ===== Completeness check finished =====
[2023-03-14 15:02:42,550] [INFO] ===== Start GTDB Search =====
[2023-03-14 15:02:42,550] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41825/markers.fasta)
[2023-03-14 15:02:42,551] [INFO] Task started: Blastn
[2023-03-14 15:02:42,552] [INFO] Running command: blastn -query OceanDNA-b41825/markers.fasta -db /var/lib/cwl/stg2a1436cf-cdae-4688-8240-cc410189caef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41825/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:02:43,708] [INFO] Task succeeded: Blastn
[2023-03-14 15:02:43,709] [INFO] Selected 19 target genomes.
[2023-03-14 15:02:43,709] [INFO] Target genome list was writen to OceanDNA-b41825/target_genomes_gtdb.txt
[2023-03-14 15:02:43,765] [INFO] Task started: fastANI
[2023-03-14 15:02:43,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a9ed0f8-3b87-4d74-80fe-362d7df24a19/OceanDNA-b41825.fa --refList OceanDNA-b41825/target_genomes_gtdb.txt --output OceanDNA-b41825/fastani_result_gtdb.tsv --threads 1
[2023-03-14 15:02:47,264] [INFO] Task succeeded: fastANI
[2023-03-14 15:02:47,269] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 15:02:47,269] [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_003282105.1	s__AG-339-G14 sp003282105	94.9059	192	272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	95.52	95.11	0.79	0.67	11	-
GCA_902613455.1	s__AG-339-G14 sp902613455	94.2682	252	272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.22	96.70	0.93	0.90	20	-
GCA_004213955.1	s__AG-339-G14 sp004213955	79.4618	114	272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616715.1	s__AG-339-G14 sp902616715	78.7337	139	272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.52	98.27	0.93	0.90	8	-
GCA_902562135.1	s__AG-339-G14 sp902562135	78.3883	112	272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.66	97.66	0.82	0.82	2	-
GCA_902536295.1	s__AG-339-G14 sp902536295	78.2277	106	272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.79	97.73	0.85	0.77	3	-
GCA_902527995.1	s__AG-339-G14 sp902527995	77.8586	87	272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 15:02:47,270] [INFO] GTDB search result was written to OceanDNA-b41825/result_gtdb.tsv
[2023-03-14 15:02:47,270] [INFO] ===== GTDB Search completed =====
[2023-03-14 15:02:47,270] [INFO] DFAST_QC result json was written to OceanDNA-b41825/dqc_result.json
[2023-03-14 15:02:47,270] [INFO] DFAST_QC completed!
[2023-03-14 15:02:47,271] [INFO] Total running time: 0h0m51s