[2023-03-19 00:33:19,077] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,077] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg19a150fd-bb72-411f-a17d-bb12df097b61/dqc_reference
[2023-03-19 00:33:20,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,244] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,244] [INFO] Running command: cat /var/lib/cwl/stg0e8fe4cb-2ebd-4905-b33c-95b40b014db7/OceanDNA-b26051.fa | prodigal -d OceanDNA-b26051/cds.fna -a OceanDNA-b26051/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:26,341] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:26,341] [INFO] Task started: HMMsearch
[2023-03-19 00:33:26,342] [INFO] Running command: hmmsearch --tblout OceanDNA-b26051/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19a150fd-bb72-411f-a17d-bb12df097b61/dqc_reference/reference_markers.hmm OceanDNA-b26051/protein.faa > /dev/null
[2023-03-19 00:33:26,535] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:26,536] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0e8fe4cb-2ebd-4905-b33c-95b40b014db7/OceanDNA-b26051.fa]
[2023-03-19 00:33:26,554] [INFO] Query marker FASTA was written to OceanDNA-b26051/markers.fasta
[2023-03-19 00:33:26,554] [INFO] Task started: Blastn
[2023-03-19 00:33:26,554] [INFO] Running command: blastn -query OceanDNA-b26051/markers.fasta -db /var/lib/cwl/stg19a150fd-bb72-411f-a17d-bb12df097b61/dqc_reference/reference_markers.fasta -out OceanDNA-b26051/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:27,080] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:27,083] [INFO] Selected 14 target genomes.
[2023-03-19 00:33:27,083] [INFO] Target genome list was writen to OceanDNA-b26051/target_genomes.txt
[2023-03-19 00:33:27,095] [INFO] Task started: fastANI
[2023-03-19 00:33:27,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e8fe4cb-2ebd-4905-b33c-95b40b014db7/OceanDNA-b26051.fa --refList OceanDNA-b26051/target_genomes.txt --output OceanDNA-b26051/fastani_result.tsv --threads 1
[2023-03-19 00:33:32,872] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:32,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19a150fd-bb72-411f-a17d-bb12df097b61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:32,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19a150fd-bb72-411f-a17d-bb12df097b61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:32,873] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:32,873] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:33:32,873] [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 00:33:32,874] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26051/tc_result.tsv
[2023-03-19 00:33:32,875] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:32,875] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:32,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19a150fd-bb72-411f-a17d-bb12df097b61/dqc_reference/checkm_data
[2023-03-19 00:33:32,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:32,886] [INFO] Task started: CheckM
[2023-03-19 00:33:32,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26051/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26051/checkm_input OceanDNA-b26051/checkm_result
[2023-03-19 00:33:54,733] [INFO] Task succeeded: CheckM
[2023-03-19 00:33:54,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 6.13%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2023-03-19 00:33:54,736] [INFO] ===== Completeness check finished =====
[2023-03-19 00:33:54,736] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:33:54,736] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26051/markers.fasta)
[2023-03-19 00:33:54,737] [INFO] Task started: Blastn
[2023-03-19 00:33:54,738] [INFO] Running command: blastn -query OceanDNA-b26051/markers.fasta -db /var/lib/cwl/stg19a150fd-bb72-411f-a17d-bb12df097b61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26051/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:55,530] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:55,532] [INFO] Selected 23 target genomes.
[2023-03-19 00:33:55,532] [INFO] Target genome list was writen to OceanDNA-b26051/target_genomes_gtdb.txt
[2023-03-19 00:33:55,587] [INFO] Task started: fastANI
[2023-03-19 00:33:55,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e8fe4cb-2ebd-4905-b33c-95b40b014db7/OceanDNA-b26051.fa --refList OceanDNA-b26051/target_genomes_gtdb.txt --output OceanDNA-b26051/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:34:01,436] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:01,446] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:34:01,446] [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_002691185.1	s__AAA536-G10 sp002691185	97.7112	213	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016777645.1	s__AAA536-G10 sp016777645	80.2444	196	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595145.1	s__AAA536-G10 sp902595145	77.5787	115	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583415.1	s__AAA536-G10 sp902583415	77.5757	105	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529515.1	s__AAA536-G10 sp902529515	77.5218	94	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.18	97.18	0.52	0.52	2	-
GCA_902578805.1	s__AAA536-G10 sp902578805	77.4764	91	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384615.1	s__AAA536-G10 sp000384615	77.3536	148	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623995.1	s__AAA536-G10 sp902623995	77.3346	142	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.83	98.83	0.84	0.84	2	-
GCA_902619615.1	s__AAA536-G10 sp902619615	77.2779	158	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284565.1	s__AAA536-G10 sp003284565	77.2464	119	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616615.1	s__AAA536-G10 sp902616615	77.2463	122	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618025.1	s__AAA536-G10 sp902618025	77.1846	112	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278095.1	s__AAA536-G10 sp003278095	77.1827	158	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.84	95.67	0.90	0.81	3	-
GCA_003283875.1	s__AAA536-G10 sp003283875	77.1741	101	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.33	95.28	0.67	0.61	3	-
GCA_016777705.1	s__AAA536-G10 sp016777705	77.0585	104	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	96.71	95.13	0.61	0.57	3	-
GCA_902530325.1	s__AAA536-G10 sp902530325	76.989	103	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514865.1	s__AAA536-G10 sp902514865	76.934	71	399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:34:01,447] [INFO] GTDB search result was written to OceanDNA-b26051/result_gtdb.tsv
[2023-03-19 00:34:01,448] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:34:01,449] [INFO] DFAST_QC result json was written to OceanDNA-b26051/dqc_result.json
[2023-03-19 00:34:01,450] [INFO] DFAST_QC completed!
[2023-03-19 00:34:01,450] [INFO] Total running time: 0h0m42s