[2023-03-15 08:11:06,014] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:11:06,015] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:11:06,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg83938a4a-6ae2-40c4-afa5-46d94c4b58ae/dqc_reference
[2023-03-15 08:11:07,119] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:11:07,119] [INFO] Task started: Prodigal
[2023-03-15 08:11:07,120] [INFO] Running command: cat /var/lib/cwl/stgc70cccde-6130-4c4a-af9c-e4c3c0a5ef4f/OceanDNA-b24487.fa | prodigal -d OceanDNA-b24487/cds.fna -a OceanDNA-b24487/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:11:11,471] [INFO] Task succeeded: Prodigal
[2023-03-15 08:11:11,472] [INFO] Task started: HMMsearch
[2023-03-15 08:11:11,472] [INFO] Running command: hmmsearch --tblout OceanDNA-b24487/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83938a4a-6ae2-40c4-afa5-46d94c4b58ae/dqc_reference/reference_markers.hmm OceanDNA-b24487/protein.faa > /dev/null
[2023-03-15 08:11:11,596] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:11:11,596] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc70cccde-6130-4c4a-af9c-e4c3c0a5ef4f/OceanDNA-b24487.fa]
[2023-03-15 08:11:11,687] [INFO] Query marker FASTA was written to OceanDNA-b24487/markers.fasta
[2023-03-15 08:11:11,688] [INFO] Task started: Blastn
[2023-03-15 08:11:11,688] [INFO] Running command: blastn -query OceanDNA-b24487/markers.fasta -db /var/lib/cwl/stg83938a4a-6ae2-40c4-afa5-46d94c4b58ae/dqc_reference/reference_markers.fasta -out OceanDNA-b24487/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:12,183] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:12,203] [INFO] Selected 12 target genomes.
[2023-03-15 08:11:12,203] [INFO] Target genome list was writen to OceanDNA-b24487/target_genomes.txt
[2023-03-15 08:11:12,211] [INFO] Task started: fastANI
[2023-03-15 08:11:12,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgc70cccde-6130-4c4a-af9c-e4c3c0a5ef4f/OceanDNA-b24487.fa --refList OceanDNA-b24487/target_genomes.txt --output OceanDNA-b24487/fastani_result.tsv --threads 1
[2023-03-15 08:11:16,968] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:16,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83938a4a-6ae2-40c4-afa5-46d94c4b58ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:11:16,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83938a4a-6ae2-40c4-afa5-46d94c4b58ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:11:16,969] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:11:16,969] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:11:16,969] [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 08:11:16,984] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24487/tc_result.tsv
[2023-03-15 08:11:17,001] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:11:17,001] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:11:17,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83938a4a-6ae2-40c4-afa5-46d94c4b58ae/dqc_reference/checkm_data
[2023-03-15 08:11:17,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:11:17,006] [INFO] Task started: CheckM
[2023-03-15 08:11:17,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24487/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24487/checkm_input OceanDNA-b24487/checkm_result
[2023-03-15 08:11:34,857] [INFO] Task succeeded: CheckM
[2023-03-15 08:11:34,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:11:34,891] [INFO] ===== Completeness check finished =====
[2023-03-15 08:11:34,891] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:11:34,891] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24487/markers.fasta)
[2023-03-15 08:11:34,892] [INFO] Task started: Blastn
[2023-03-15 08:11:34,892] [INFO] Running command: blastn -query OceanDNA-b24487/markers.fasta -db /var/lib/cwl/stg83938a4a-6ae2-40c4-afa5-46d94c4b58ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24487/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:35,551] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:35,588] [INFO] Selected 15 target genomes.
[2023-03-15 08:11:35,588] [INFO] Target genome list was writen to OceanDNA-b24487/target_genomes_gtdb.txt
[2023-03-15 08:11:35,596] [INFO] Task started: fastANI
[2023-03-15 08:11:35,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgc70cccde-6130-4c4a-af9c-e4c3c0a5ef4f/OceanDNA-b24487.fa --refList OceanDNA-b24487/target_genomes_gtdb.txt --output OceanDNA-b24487/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:11:38,469] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:38,478] [INFO] Found 15 fastANI hits (4 hits with ANI > circumscription radius)
[2023-03-15 08:11:38,478] [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_902599045.1	s__HIMB59 sp902615815	97.0045	181	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.41	95.18	0.86	0.81	23	inconclusive
GCA_902557145.1	s__HIMB59 sp902557145	96.5041	182	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.38	95.38	0.79	0.79	2	inconclusive
GCA_902601865.1	s__HIMB59 sp902601865	95.9835	170	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902514885.1	s__HIMB59 sp902514885	95.1314	106	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.68	95.68	0.76	0.76	2	inconclusive
GCA_902521795.1	s__HIMB59 sp902560595	94.3145	159	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.49	95.27	0.76	0.73	4	-
GCA_902526965.1	s__HIMB59 sp902526965	93.7879	151	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528805.1	s__HIMB59 sp902528805	93.5962	134	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902610415.1	s__HIMB59 sp902610415	93.1318	140	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.41	95.41	0.66	0.66	2	-
GCA_902516235.1	s__HIMB59 sp902516235	92.3698	147	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546975.1	s__HIMB59 sp902546975	83.0649	154	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.15	95.57	0.84	0.81	5	-
GCA_902616855.1	s__HIMB59 sp902616855	82.6434	152	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.19	95.15	0.77	0.74	3	-
GCA_902538085.1	s__HIMB59 sp902538085	82.6241	164	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.32	95.03	0.79	0.77	3	-
GCA_902595525.1	s__HIMB59 sp902595525	82.5046	96	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542505.1	s__HIMB59 sp902542505	82.3703	89	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.42	95.42	0.57	0.57	2	-
GCA_902617515.1	s__HIMB59 sp902617515	82.2194	117	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:11:38,479] [INFO] GTDB search result was written to OceanDNA-b24487/result_gtdb.tsv
[2023-03-15 08:11:38,479] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:11:38,480] [INFO] DFAST_QC result json was written to OceanDNA-b24487/dqc_result.json
[2023-03-15 08:11:38,480] [INFO] DFAST_QC completed!
[2023-03-15 08:11:38,480] [INFO] Total running time: 0h0m32s