[2023-03-16 19:49:08,451] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:49:08,452] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:49:08,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgf24bed26-78fa-4331-9c59-a8836925ba82/dqc_reference
[2023-03-16 19:49:09,532] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:49:09,533] [INFO] Task started: Prodigal
[2023-03-16 19:49:09,533] [INFO] Running command: cat /var/lib/cwl/stgffd7767b-2530-40c7-b1af-dfd8dcd7ccbd/OceanDNA-b16537.fa | prodigal -d OceanDNA-b16537/cds.fna -a OceanDNA-b16537/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:49:19,955] [INFO] Task succeeded: Prodigal
[2023-03-16 19:49:19,955] [INFO] Task started: HMMsearch
[2023-03-16 19:49:19,955] [INFO] Running command: hmmsearch --tblout OceanDNA-b16537/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf24bed26-78fa-4331-9c59-a8836925ba82/dqc_reference/reference_markers.hmm OceanDNA-b16537/protein.faa > /dev/null
[2023-03-16 19:49:20,082] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:49:20,082] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgffd7767b-2530-40c7-b1af-dfd8dcd7ccbd/OceanDNA-b16537.fa]
[2023-03-16 19:49:20,096] [INFO] Query marker FASTA was written to OceanDNA-b16537/markers.fasta
[2023-03-16 19:49:20,097] [INFO] Task started: Blastn
[2023-03-16 19:49:20,097] [INFO] Running command: blastn -query OceanDNA-b16537/markers.fasta -db /var/lib/cwl/stgf24bed26-78fa-4331-9c59-a8836925ba82/dqc_reference/reference_markers.fasta -out OceanDNA-b16537/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:49:20,545] [INFO] Task succeeded: Blastn
[2023-03-16 19:49:20,547] [INFO] Selected 18 target genomes.
[2023-03-16 19:49:20,547] [INFO] Target genome list was writen to OceanDNA-b16537/target_genomes.txt
[2023-03-16 19:49:20,558] [INFO] Task started: fastANI
[2023-03-16 19:49:20,558] [INFO] Running command: fastANI --query /var/lib/cwl/stgffd7767b-2530-40c7-b1af-dfd8dcd7ccbd/OceanDNA-b16537.fa --refList OceanDNA-b16537/target_genomes.txt --output OceanDNA-b16537/fastani_result.tsv --threads 1
[2023-03-16 19:49:31,369] [INFO] Task succeeded: fastANI
[2023-03-16 19:49:31,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf24bed26-78fa-4331-9c59-a8836925ba82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:49:31,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf24bed26-78fa-4331-9c59-a8836925ba82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:49:31,372] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:49:31,373] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:49:31,373] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	84.9052	239	279	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:49:31,373] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16537/tc_result.tsv
[2023-03-16 19:49:31,373] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:49:31,373] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:49:31,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf24bed26-78fa-4331-9c59-a8836925ba82/dqc_reference/checkm_data
[2023-03-16 19:49:31,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:49:31,389] [INFO] Task started: CheckM
[2023-03-16 19:49:31,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16537/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16537/checkm_input OceanDNA-b16537/checkm_result
[2023-03-16 19:50:03,129] [INFO] Task succeeded: CheckM
[2023-03-16 19:50:03,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.86%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 19:50:03,132] [INFO] ===== Completeness check finished =====
[2023-03-16 19:50:03,132] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:50:03,132] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16537/markers.fasta)
[2023-03-16 19:50:03,133] [INFO] Task started: Blastn
[2023-03-16 19:50:03,133] [INFO] Running command: blastn -query OceanDNA-b16537/markers.fasta -db /var/lib/cwl/stgf24bed26-78fa-4331-9c59-a8836925ba82/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16537/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:50:03,631] [INFO] Task succeeded: Blastn
[2023-03-16 19:50:03,632] [INFO] Selected 10 target genomes.
[2023-03-16 19:50:03,633] [INFO] Target genome list was writen to OceanDNA-b16537/target_genomes_gtdb.txt
[2023-03-16 19:50:03,642] [INFO] Task started: fastANI
[2023-03-16 19:50:03,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgffd7767b-2530-40c7-b1af-dfd8dcd7ccbd/OceanDNA-b16537.fa --refList OceanDNA-b16537/target_genomes_gtdb.txt --output OceanDNA-b16537/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:50:06,927] [INFO] Task succeeded: fastANI
[2023-03-16 19:50:06,933] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 19:50:06,934] [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_003211535.1	s__Synechococcus_E sp003211535	88.3305	203	279	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280175.1	s__Synechococcus_E sp004212765	86.0045	236	279	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.21	96.96	0.98	0.97	4	-
GCF_014280195.1	s__Synechococcus_E sp014280195	85.0074	240	279	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195975.1	s__Synechococcus_E sp000195975	84.9052	239	279	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.37	97.74	0.92	0.91	7	-
GCA_002170825.1	s__Synechococcus_E sp002170825	79.035	116	279	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.06	98.06	0.77	0.77	2	-
GCF_014279895.1	s__Synechococcus_E sp002724845	78.5844	137	279	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
GCF_000012625.1	s__Synechococcus_E sp000012625	78.3063	128	279	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.15	95.15	0.92	0.92	2	-
GCA_002700765.1	s__Synechococcus_E sp002700765	77.6022	83	279	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003211235.1	s__Synechococcus_E sp003211235	77.2124	53	279	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:50:06,934] [INFO] GTDB search result was written to OceanDNA-b16537/result_gtdb.tsv
[2023-03-16 19:50:06,934] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:50:06,936] [INFO] DFAST_QC result json was written to OceanDNA-b16537/dqc_result.json
[2023-03-16 19:50:06,936] [INFO] DFAST_QC completed!
[2023-03-16 19:50:06,936] [INFO] Total running time: 0h0m58s