[2023-03-16 23:55:45,907] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:55:45,915] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:55:45,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d50d029-bbcb-4bfa-b166-64e679d6306e/dqc_reference
[2023-03-16 23:55:47,049] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:55:47,049] [INFO] Task started: Prodigal
[2023-03-16 23:55:47,049] [INFO] Running command: cat /var/lib/cwl/stg54ec05e2-b717-4709-81b7-f5dad562b280/OceanDNA-b16544.fa | prodigal -d OceanDNA-b16544/cds.fna -a OceanDNA-b16544/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:56:00,169] [INFO] Task succeeded: Prodigal
[2023-03-16 23:56:00,170] [INFO] Task started: HMMsearch
[2023-03-16 23:56:00,170] [INFO] Running command: hmmsearch --tblout OceanDNA-b16544/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d50d029-bbcb-4bfa-b166-64e679d6306e/dqc_reference/reference_markers.hmm OceanDNA-b16544/protein.faa > /dev/null
[2023-03-16 23:56:00,350] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:56:00,350] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg54ec05e2-b717-4709-81b7-f5dad562b280/OceanDNA-b16544.fa]
[2023-03-16 23:56:00,497] [INFO] Query marker FASTA was written to OceanDNA-b16544/markers.fasta
[2023-03-16 23:56:00,498] [INFO] Task started: Blastn
[2023-03-16 23:56:00,498] [INFO] Running command: blastn -query OceanDNA-b16544/markers.fasta -db /var/lib/cwl/stg4d50d029-bbcb-4bfa-b166-64e679d6306e/dqc_reference/reference_markers.fasta -out OceanDNA-b16544/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:56:01,072] [INFO] Task succeeded: Blastn
[2023-03-16 23:56:01,119] [INFO] Selected 15 target genomes.
[2023-03-16 23:56:01,119] [INFO] Target genome list was writen to OceanDNA-b16544/target_genomes.txt
[2023-03-16 23:56:01,131] [INFO] Task started: fastANI
[2023-03-16 23:56:01,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg54ec05e2-b717-4709-81b7-f5dad562b280/OceanDNA-b16544.fa --refList OceanDNA-b16544/target_genomes.txt --output OceanDNA-b16544/fastani_result.tsv --threads 1
[2023-03-16 23:56:12,560] [INFO] Task succeeded: fastANI
[2023-03-16 23:56:12,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d50d029-bbcb-4bfa-b166-64e679d6306e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:56:12,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d50d029-bbcb-4bfa-b166-64e679d6306e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:56:12,565] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:56:12,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:56:12,565] [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	86.685	414	446	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:56:12,569] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16544/tc_result.tsv
[2023-03-16 23:56:12,575] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:56:12,575] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:56:12,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d50d029-bbcb-4bfa-b166-64e679d6306e/dqc_reference/checkm_data
[2023-03-16 23:56:12,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:56:12,582] [INFO] Task started: CheckM
[2023-03-16 23:56:12,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16544/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16544/checkm_input OceanDNA-b16544/checkm_result
[2023-03-16 23:56:43,974] [INFO] Task succeeded: CheckM
[2023-03-16 23:56:43,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:56:44,144] [INFO] ===== Completeness check finished =====
[2023-03-16 23:56:44,144] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:56:44,144] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16544/markers.fasta)
[2023-03-16 23:56:44,145] [INFO] Task started: Blastn
[2023-03-16 23:56:44,146] [INFO] Running command: blastn -query OceanDNA-b16544/markers.fasta -db /var/lib/cwl/stg4d50d029-bbcb-4bfa-b166-64e679d6306e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16544/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:56:45,078] [INFO] Task succeeded: Blastn
[2023-03-16 23:56:45,088] [INFO] Selected 10 target genomes.
[2023-03-16 23:56:45,088] [INFO] Target genome list was writen to OceanDNA-b16544/target_genomes_gtdb.txt
[2023-03-16 23:56:45,302] [INFO] Task started: fastANI
[2023-03-16 23:56:45,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg54ec05e2-b717-4709-81b7-f5dad562b280/OceanDNA-b16544.fa --refList OceanDNA-b16544/target_genomes_gtdb.txt --output OceanDNA-b16544/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:56:49,239] [INFO] Task succeeded: fastANI
[2023-03-16 23:56:49,246] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:56:49,246] [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
GCF_014280175.1	s__Synechococcus_E sp004212765	98.6894	437	446	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	conclusive
GCF_000195975.1	s__Synechococcus_E sp000195975	86.685	414	446	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	-
GCF_014280195.1	s__Synechococcus_E sp014280195	86.6426	426	446	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	-
GCA_003211535.1	s__Synechococcus_E sp003211535	85.181	333	446	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_014279895.1	s__Synechococcus_E sp002724845	80.617	286	446	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	-
GCA_013911515.1	s__Synechococcus_E sp013911515	80.3283	235	446	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_000161795.2	s__Synechococcus_E sp000161795	80.1777	277	446	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	-
GCA_002170825.1	s__Synechococcus_E sp002170825	79.9278	207	446	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	-
GCA_016779825.1	s__Synechococcus_E sp016779825	79.8399	227	446	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	-
GCA_003210735.1	s__Synechococcus_E sp003210735	78.8918	185	446	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.42	95.39	0.68	0.68	3	-
--------------------------------------------------------------------------------
[2023-03-16 23:56:49,251] [INFO] GTDB search result was written to OceanDNA-b16544/result_gtdb.tsv
[2023-03-16 23:56:49,254] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:56:49,260] [INFO] DFAST_QC result json was written to OceanDNA-b16544/dqc_result.json
[2023-03-16 23:56:49,260] [INFO] DFAST_QC completed!
[2023-03-16 23:56:49,260] [INFO] Total running time: 0h1m3s