[2023-03-18 23:27:53,697] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,699] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg1da99525-b15e-447b-bf97-61d1017895a7/dqc_reference
[2023-03-18 23:27:55,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,546] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,546] [INFO] Running command: cat /var/lib/cwl/stg3e443437-d9de-45ec-8400-e149e8ed3262/OceanDNA-b18214.fa | prodigal -d OceanDNA-b18214/cds.fna -a OceanDNA-b18214/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:27:59,839] [INFO] Task succeeded: Prodigal
[2023-03-18 23:27:59,839] [INFO] Task started: HMMsearch
[2023-03-18 23:27:59,839] [INFO] Running command: hmmsearch --tblout OceanDNA-b18214/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1da99525-b15e-447b-bf97-61d1017895a7/dqc_reference/reference_markers.hmm OceanDNA-b18214/protein.faa > /dev/null
[2023-03-18 23:28:00,040] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:00,041] [INFO] Found 6/6 markers.
[2023-03-18 23:28:00,048] [INFO] Query marker FASTA was written to OceanDNA-b18214/markers.fasta
[2023-03-18 23:28:00,048] [INFO] Task started: Blastn
[2023-03-18 23:28:00,048] [INFO] Running command: blastn -query OceanDNA-b18214/markers.fasta -db /var/lib/cwl/stg1da99525-b15e-447b-bf97-61d1017895a7/dqc_reference/reference_markers.fasta -out OceanDNA-b18214/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:01,504] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:01,505] [INFO] Selected 16 target genomes.
[2023-03-18 23:28:01,505] [INFO] Target genome list was writen to OceanDNA-b18214/target_genomes.txt
[2023-03-18 23:28:01,517] [INFO] Task started: fastANI
[2023-03-18 23:28:01,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e443437-d9de-45ec-8400-e149e8ed3262/OceanDNA-b18214.fa --refList OceanDNA-b18214/target_genomes.txt --output OceanDNA-b18214/fastani_result.tsv --threads 1
[2023-03-18 23:28:07,599] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:07,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1da99525-b15e-447b-bf97-61d1017895a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:07,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1da99525-b15e-447b-bf97-61d1017895a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:07,600] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:07,600] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:28:07,600] [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 23:28:07,600] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18214/tc_result.tsv
[2023-03-18 23:28:07,600] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:07,600] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:07,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1da99525-b15e-447b-bf97-61d1017895a7/dqc_reference/checkm_data
[2023-03-18 23:28:07,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:07,650] [INFO] Task started: CheckM
[2023-03-18 23:28:07,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18214/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18214/checkm_input OceanDNA-b18214/checkm_result
[2023-03-18 23:28:24,869] [INFO] Task succeeded: CheckM
[2023-03-18 23:28:24,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:28:24,871] [INFO] ===== Completeness check finished =====
[2023-03-18 23:28:24,871] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:28:24,871] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18214/markers.fasta)
[2023-03-18 23:28:24,871] [INFO] Task started: Blastn
[2023-03-18 23:28:24,871] [INFO] Running command: blastn -query OceanDNA-b18214/markers.fasta -db /var/lib/cwl/stg1da99525-b15e-447b-bf97-61d1017895a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18214/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:25,576] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:25,577] [INFO] Selected 12 target genomes.
[2023-03-18 23:28:25,577] [INFO] Target genome list was writen to OceanDNA-b18214/target_genomes_gtdb.txt
[2023-03-18 23:28:25,590] [INFO] Task started: fastANI
[2023-03-18 23:28:25,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e443437-d9de-45ec-8400-e149e8ed3262/OceanDNA-b18214.fa --refList OceanDNA-b18214/target_genomes_gtdb.txt --output OceanDNA-b18214/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:28:28,693] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:28,698] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:28:28,698] [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_000402815.1	s__Marinisoma atlanticum	99.2604	264	279	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	conclusive
GCA_002701645.1	s__Marinisoma sp002701645	83.9852	171	279	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182795.1	s__Marinisoma sp905182795	83.854	243	279	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240005.1	s__Marinisoma sp014240005	83.6068	196	279	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.63	96.63	0.87	0.87	2	-
GCA_000402755.1	s__Marinisoma sp000402755	83.4185	225	279	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	95.42	95.16	0.79	0.76	17	-
GCA_902629855.1	s__Marinisoma sp902629855	78.1416	82	279	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	98.59	98.03	0.85	0.83	5	-
GCA_902578385.1	s__Marinisoma sp002710515	78.1091	86	279	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
--------------------------------------------------------------------------------
[2023-03-18 23:28:28,698] [INFO] GTDB search result was written to OceanDNA-b18214/result_gtdb.tsv
[2023-03-18 23:28:28,699] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:28:28,699] [INFO] DFAST_QC result json was written to OceanDNA-b18214/dqc_result.json
[2023-03-18 23:28:28,699] [INFO] DFAST_QC completed!
[2023-03-18 23:28:28,699] [INFO] Total running time: 0h0m35s