[2023-03-19 05:19:33,740] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg70c127fd-b66d-4e20-92c1-f29ede48b49c/dqc_reference
[2023-03-19 05:19:35,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,407] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,407] [INFO] Running command: cat /var/lib/cwl/stg3431dbd7-d38f-448a-91f5-d1506dc1886b/OceanDNA-b18033.fa | prodigal -d OceanDNA-b18033/cds.fna -a OceanDNA-b18033/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:39,233] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:39,233] [INFO] Task started: HMMsearch
[2023-03-19 05:19:39,233] [INFO] Running command: hmmsearch --tblout OceanDNA-b18033/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70c127fd-b66d-4e20-92c1-f29ede48b49c/dqc_reference/reference_markers.hmm OceanDNA-b18033/protein.faa > /dev/null
[2023-03-19 05:19:39,486] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:39,486] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3431dbd7-d38f-448a-91f5-d1506dc1886b/OceanDNA-b18033.fa]
[2023-03-19 05:19:39,492] [INFO] Query marker FASTA was written to OceanDNA-b18033/markers.fasta
[2023-03-19 05:19:39,493] [INFO] Task started: Blastn
[2023-03-19 05:19:39,493] [INFO] Running command: blastn -query OceanDNA-b18033/markers.fasta -db /var/lib/cwl/stg70c127fd-b66d-4e20-92c1-f29ede48b49c/dqc_reference/reference_markers.fasta -out OceanDNA-b18033/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:39,997] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:39,998] [INFO] Selected 11 target genomes.
[2023-03-19 05:19:39,998] [INFO] Target genome list was writen to OceanDNA-b18033/target_genomes.txt
[2023-03-19 05:19:40,005] [INFO] Task started: fastANI
[2023-03-19 05:19:40,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg3431dbd7-d38f-448a-91f5-d1506dc1886b/OceanDNA-b18033.fa --refList OceanDNA-b18033/target_genomes.txt --output OceanDNA-b18033/fastani_result.tsv --threads 1
[2023-03-19 05:19:44,612] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:44,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70c127fd-b66d-4e20-92c1-f29ede48b49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:44,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70c127fd-b66d-4e20-92c1-f29ede48b49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:19:44,612] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:19:44,613] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:19:44,613] [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
--------------------------------------------------------------------------------
[2023-03-19 05:19:44,613] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18033/tc_result.tsv
[2023-03-19 05:19:44,613] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:19:44,613] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:44,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70c127fd-b66d-4e20-92c1-f29ede48b49c/dqc_reference/checkm_data
[2023-03-19 05:19:44,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:44,618] [INFO] Task started: CheckM
[2023-03-19 05:19:44,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18033/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18033/checkm_input OceanDNA-b18033/checkm_result
[2023-03-19 05:20:00,365] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:00,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:00,372] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:00,372] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:00,372] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18033/markers.fasta)
[2023-03-19 05:20:00,373] [INFO] Task started: Blastn
[2023-03-19 05:20:00,373] [INFO] Running command: blastn -query OceanDNA-b18033/markers.fasta -db /var/lib/cwl/stg70c127fd-b66d-4e20-92c1-f29ede48b49c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18033/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:00,982] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:00,987] [INFO] Selected 11 target genomes.
[2023-03-19 05:20:00,988] [INFO] Target genome list was writen to OceanDNA-b18033/target_genomes_gtdb.txt
[2023-03-19 05:20:01,048] [INFO] Task started: fastANI
[2023-03-19 05:20:01,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg3431dbd7-d38f-448a-91f5-d1506dc1886b/OceanDNA-b18033.fa --refList OceanDNA-b18033/target_genomes_gtdb.txt --output OceanDNA-b18033/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:03,212] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:03,218] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:20:03,218] [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_014240005.1	s__Marinisoma sp014240005	84.1788	180	239	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.63	96.63	0.87	0.87	2	-
GCA_002701645.1	s__Marinisoma sp002701645	83.4434	153	239	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	82.5759	201	239	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402755.1	s__Marinisoma sp000402755	82.1607	175	239	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	95.42	95.16	0.79	0.76	17	-
GCA_000402815.1	s__Marinisoma atlanticum	81.579	182	239	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_902578385.1	s__Marinisoma sp002710515	77.9116	63	239	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
GCA_902599655.1	s__Marinisoma sp902599655	77.673	54	239	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.53	97.28	0.66	0.66	3	-
GCA_000402655.1	s__Marinisoma sp000402655	77.565	75	239	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
GCA_902629855.1	s__Marinisoma sp902629855	77.5422	61	239	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	98.59	98.03	0.85	0.83	5	-
GCA_012963075.1	s__Marinisoma sp012963075	77.469	71	239	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:03,219] [INFO] GTDB search result was written to OceanDNA-b18033/result_gtdb.tsv
[2023-03-19 05:20:03,219] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:03,220] [INFO] DFAST_QC result json was written to OceanDNA-b18033/dqc_result.json
[2023-03-19 05:20:03,220] [INFO] DFAST_QC completed!
[2023-03-19 05:20:03,220] [INFO] Total running time: 0h0m29s