[2023-03-19 03:28:07,275] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:28:07,275] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:28:07,275] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe503511-60e9-4327-bee9-9570b11600a8/dqc_reference
[2023-03-19 03:28:08,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:28:08,369] [INFO] Task started: Prodigal
[2023-03-19 03:28:08,369] [INFO] Running command: cat /var/lib/cwl/stg47f8f62c-1e62-4265-857f-19eea54c0eb1/OceanDNA-b16309.fa | prodigal -d OceanDNA-b16309/cds.fna -a OceanDNA-b16309/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:28:12,462] [INFO] Task succeeded: Prodigal
[2023-03-19 03:28:12,462] [INFO] Task started: HMMsearch
[2023-03-19 03:28:12,462] [INFO] Running command: hmmsearch --tblout OceanDNA-b16309/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe503511-60e9-4327-bee9-9570b11600a8/dqc_reference/reference_markers.hmm OceanDNA-b16309/protein.faa > /dev/null
[2023-03-19 03:28:12,596] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:28:12,596] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg47f8f62c-1e62-4265-857f-19eea54c0eb1/OceanDNA-b16309.fa]
[2023-03-19 03:28:12,605] [INFO] Query marker FASTA was written to OceanDNA-b16309/markers.fasta
[2023-03-19 03:28:12,606] [INFO] Task started: Blastn
[2023-03-19 03:28:12,607] [INFO] Running command: blastn -query OceanDNA-b16309/markers.fasta -db /var/lib/cwl/stgbe503511-60e9-4327-bee9-9570b11600a8/dqc_reference/reference_markers.fasta -out OceanDNA-b16309/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:28:13,106] [INFO] Task succeeded: Blastn
[2023-03-19 03:28:13,107] [INFO] Selected 11 target genomes.
[2023-03-19 03:28:13,107] [INFO] Target genome list was writen to OceanDNA-b16309/target_genomes.txt
[2023-03-19 03:28:13,113] [INFO] Task started: fastANI
[2023-03-19 03:28:13,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f8f62c-1e62-4265-857f-19eea54c0eb1/OceanDNA-b16309.fa --refList OceanDNA-b16309/target_genomes.txt --output OceanDNA-b16309/fastani_result.tsv --threads 1
[2023-03-19 03:28:15,993] [INFO] Task succeeded: fastANI
[2023-03-19 03:28:15,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe503511-60e9-4327-bee9-9570b11600a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:28:15,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe503511-60e9-4327-bee9-9570b11600a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:28:15,994] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:28:15,994] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:28:15,994] [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 03:28:15,994] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16309/tc_result.tsv
[2023-03-19 03:28:15,994] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:28:15,994] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:28:15,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe503511-60e9-4327-bee9-9570b11600a8/dqc_reference/checkm_data
[2023-03-19 03:28:16,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:28:16,044] [INFO] Task started: CheckM
[2023-03-19 03:28:16,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16309/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16309/checkm_input OceanDNA-b16309/checkm_result
[2023-03-19 03:28:32,672] [INFO] Task succeeded: CheckM
[2023-03-19 03:28:32,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.46%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:28:32,674] [INFO] ===== Completeness check finished =====
[2023-03-19 03:28:32,674] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:28:32,675] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16309/markers.fasta)
[2023-03-19 03:28:32,676] [INFO] Task started: Blastn
[2023-03-19 03:28:32,676] [INFO] Running command: blastn -query OceanDNA-b16309/markers.fasta -db /var/lib/cwl/stgbe503511-60e9-4327-bee9-9570b11600a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16309/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:28:33,563] [INFO] Task succeeded: Blastn
[2023-03-19 03:28:33,564] [INFO] Selected 19 target genomes.
[2023-03-19 03:28:33,564] [INFO] Target genome list was writen to OceanDNA-b16309/target_genomes_gtdb.txt
[2023-03-19 03:28:33,618] [INFO] Task started: fastANI
[2023-03-19 03:28:33,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f8f62c-1e62-4265-857f-19eea54c0eb1/OceanDNA-b16309.fa --refList OceanDNA-b16309/target_genomes_gtdb.txt --output OceanDNA-b16309/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:28:37,747] [INFO] Task succeeded: fastANI
[2023-03-19 03:28:37,758] [INFO] Found 19 fastANI hits (16 hits with ANI > circumscription radius)
[2023-03-19 03:28:37,759] [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_000635495.1	s__Prochlorococcus_A sp000635495	97.3157	185	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	98.33	95.15	0.88	0.77	73	inconclusive
GCA_000634735.1	s__Prochlorococcus_A sp000634735	96.84	173	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	97.92	96.63	0.82	0.80	7	inconclusive
GCA_003278705.1	s__Prochlorococcus_A sp003278705	96.786	166	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	97.00	97.00	0.89	0.89	2	inconclusive
GCA_000634195.1	s__Prochlorococcus_A sp000634195	96.5997	138	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_003280655.1	s__Prochlorococcus_A sp003280655	96.4822	189	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	97.89	97.33	0.89	0.82	6	inconclusive
GCA_003280895.1	s__Prochlorococcus_A sp003280895	96.0994	164	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902621675.1	s__Prochlorococcus_A sp902621675	96.0013	133	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902616385.1	s__Prochlorococcus_A sp902616385	95.9171	175	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000015965.1	s__Prochlorococcus_A marinus_E	95.8234	196	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	98.13	98.13	0.90	0.90	2	inconclusive
GCA_000635535.1	s__Prochlorococcus_A sp000635535	95.7602	108	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_003216915.1	s__Prochlorococcus_A sp003216915	95.6849	168	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902537445.1	s__Prochlorococcus_A sp902537445	95.4783	130	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_017696055.1	s__Prochlorococcus_A marinus_W	95.1641	193	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	100.00	100.00	1.00	1.00	2	inconclusive
GCA_003214115.1	s__Prochlorococcus_A sp003214115	95.1426	131	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_003211415.1	s__Prochlorococcus_A sp003211415	95.0891	124	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.46	95.46	0.66	0.66	2	inconclusive
GCA_003279055.1	s__Prochlorococcus_A sp003279055	95.0536	183	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902558895.1	s__Prochlorococcus_A sp902558895	94.966	131	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606505.1	s__Prochlorococcus_A sp902606505	94.9124	143	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644375.1	s__Prochlorococcus_A marinus_AH	94.0205	192	197	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:28:37,759] [INFO] GTDB search result was written to OceanDNA-b16309/result_gtdb.tsv
[2023-03-19 03:28:37,759] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:28:37,760] [INFO] DFAST_QC result json was written to OceanDNA-b16309/dqc_result.json
[2023-03-19 03:28:37,760] [INFO] DFAST_QC completed!
[2023-03-19 03:28:37,760] [INFO] Total running time: 0h0m30s