[2023-03-18 10:02:11,408] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:02:11,408] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:02:11,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ebd5206-5b77-4285-a4d8-98469900f2bc/dqc_reference
[2023-03-18 10:02:12,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:02:12,534] [INFO] Task started: Prodigal
[2023-03-18 10:02:12,534] [INFO] Running command: cat /var/lib/cwl/stg39c19b7f-698e-4799-9577-6cd590ecafc8/OceanDNA-b16280.fa | prodigal -d OceanDNA-b16280/cds.fna -a OceanDNA-b16280/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:02:18,625] [INFO] Task succeeded: Prodigal
[2023-03-18 10:02:18,625] [INFO] Task started: HMMsearch
[2023-03-18 10:02:18,625] [INFO] Running command: hmmsearch --tblout OceanDNA-b16280/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ebd5206-5b77-4285-a4d8-98469900f2bc/dqc_reference/reference_markers.hmm OceanDNA-b16280/protein.faa > /dev/null
[2023-03-18 10:02:18,797] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:02:18,797] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg39c19b7f-698e-4799-9577-6cd590ecafc8/OceanDNA-b16280.fa]
[2023-03-18 10:02:18,806] [INFO] Query marker FASTA was written to OceanDNA-b16280/markers.fasta
[2023-03-18 10:02:18,806] [INFO] Task started: Blastn
[2023-03-18 10:02:18,806] [INFO] Running command: blastn -query OceanDNA-b16280/markers.fasta -db /var/lib/cwl/stg7ebd5206-5b77-4285-a4d8-98469900f2bc/dqc_reference/reference_markers.fasta -out OceanDNA-b16280/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:02:19,297] [INFO] Task succeeded: Blastn
[2023-03-18 10:02:19,298] [INFO] Selected 22 target genomes.
[2023-03-18 10:02:19,298] [INFO] Target genome list was writen to OceanDNA-b16280/target_genomes.txt
[2023-03-18 10:02:19,309] [INFO] Task started: fastANI
[2023-03-18 10:02:19,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg39c19b7f-698e-4799-9577-6cd590ecafc8/OceanDNA-b16280.fa --refList OceanDNA-b16280/target_genomes.txt --output OceanDNA-b16280/fastani_result.tsv --threads 1
[2023-03-18 10:02:28,182] [INFO] Task succeeded: fastANI
[2023-03-18 10:02:28,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ebd5206-5b77-4285-a4d8-98469900f2bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:02:28,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ebd5206-5b77-4285-a4d8-98469900f2bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:02:28,183] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:02:28,183] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:02:28,183] [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
--------------------------------------------------------------------------------
[2023-03-18 10:02:28,183] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16280/tc_result.tsv
[2023-03-18 10:02:28,183] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:02:28,183] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:02:28,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ebd5206-5b77-4285-a4d8-98469900f2bc/dqc_reference/checkm_data
[2023-03-18 10:02:28,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:02:28,188] [INFO] Task started: CheckM
[2023-03-18 10:02:28,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16280/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16280/checkm_input OceanDNA-b16280/checkm_result
[2023-03-18 10:02:48,782] [INFO] Task succeeded: CheckM
[2023-03-18 10:02:48,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 10:02:48,784] [INFO] ===== Completeness check finished =====
[2023-03-18 10:02:48,784] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:02:48,785] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16280/markers.fasta)
[2023-03-18 10:02:48,785] [INFO] Task started: Blastn
[2023-03-18 10:02:48,785] [INFO] Running command: blastn -query OceanDNA-b16280/markers.fasta -db /var/lib/cwl/stg7ebd5206-5b77-4285-a4d8-98469900f2bc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16280/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:02:49,461] [INFO] Task succeeded: Blastn
[2023-03-18 10:02:49,462] [INFO] Selected 36 target genomes.
[2023-03-18 10:02:49,462] [INFO] Target genome list was writen to OceanDNA-b16280/target_genomes_gtdb.txt
[2023-03-18 10:02:49,491] [INFO] Task started: fastANI
[2023-03-18 10:02:49,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg39c19b7f-698e-4799-9577-6cd590ecafc8/OceanDNA-b16280.fa --refList OceanDNA-b16280/target_genomes_gtdb.txt --output OceanDNA-b16280/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:02:57,781] [INFO] Task succeeded: fastANI
[2023-03-18 10:02:57,800] [INFO] Found 36 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:02:57,800] [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_000218705.1	s__Prochlorococcus_A marinus_Q	77.3611	144	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.95	95.40	0.90	0.85	14	-
GCA_003214355.1	s__Prochlorococcus_A sp003214355	77.3193	103	341	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_000218745.1	s__Prochlorococcus_A marinus_T	77.3174	133	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.73	95.11	0.87	0.85	4	-
GCF_002025975.1	s__Prochlorococcus_A sp002025975	77.0721	59	341	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_003214175.1	s__Prochlorococcus_A sp003214175	77.0718	86	341	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_003281455.1	s__Prochlorococcus_A sp003281455	77.0568	100	341	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_902624085.1	s__Prochlorococcus_A sp902624085	77.0129	93	341	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_003209585.1	s__Prochlorococcus_A sp003209585	77.0111	90	341	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_003211115.1	s__Prochlorococcus_A sp003211115	77.0106	70	341	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_003210285.1	s__Prochlorococcus_A sp003210285	77.0054	104	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	97.88	97.67	0.88	0.87	3	-
GCA_003216135.1	s__Prochlorococcus_A sp003216135	76.9979	56	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.34	95.10	0.71	0.64	4	-
GCF_000015665.1	s__Prochlorococcus_A marinus_P	76.9544	107	341	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	-
GCF_017696175.1	s__Prochlorococcus_A marinus_X	76.9536	118	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCA_003281605.1	s__Prochlorococcus_A sp003281605	76.951	103	341	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	-
GCF_017695965.1	s__Prochlorococcus_A sp003212755	76.9349	105	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0087	96.80	96.80	0.92	0.92	2	-
GCA_003279535.1	s__Prochlorococcus_A sp003279535	76.9281	83	341	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_003279935.1	s__Prochlorococcus_A sp003279935	76.9132	86	341	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	-
GCF_000760095.1	s__Prochlorococcus_A marinus_I	76.9082	100	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	99.98	99.96	0.98	0.98	3	-
GCA_003283415.1	s__Prochlorococcus_A sp003283415	76.8793	89	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	96.62	96.62	0.73	0.73	2	-
GCA_003279875.1	s__Prochlorococcus_A sp003279875	76.8544	87	341	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_003280025.1	s__Prochlorococcus_A sp003280025	76.8511	101	341	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_003209565.1	s__Prochlorococcus_A sp003209565	76.8466	88	341	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_000634735.1	s__Prochlorococcus_A sp000634735	76.8233	93	341	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	-
GCA_003214315.1	s__Prochlorococcus_A sp003214315	76.8076	92	341	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_003210915.1	s__Prochlorococcus_A sp003210915	76.8044	80	341	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	-
GCF_017696205.1	s__Prochlorococcus_A marinus_AC	76.8014	111	341	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_000291825.1	s__Prochlorococcus_A sp000291825	76.7535	68	341	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_003280655.1	s__Prochlorococcus_A sp003280655	76.7477	96	341	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	-
GCA_902627335.1	s__Prochlorococcus_A sp902627335	76.7053	105	341	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_003216795.1	s__Prochlorococcus_A sp003216795	76.6852	84	341	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_003279945.1	s__Prochlorococcus_A sp003279945	76.6824	98	341	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_003279855.1	s__Prochlorococcus_A sp003279855	76.676	112	341	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_003212375.1	s__Prochlorococcus_A sp003212375	76.6042	81	341	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_003216465.1	s__Prochlorococcus_A sp003216465	76.6041	112	341	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_003210275.1	s__Prochlorococcus_A sp003210275	76.5412	70	341	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	-
GCF_000012645.1	s__Prochlorococcus_A marinus_L	76.3992	110	341	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	-
--------------------------------------------------------------------------------
[2023-03-18 10:02:57,800] [INFO] GTDB search result was written to OceanDNA-b16280/result_gtdb.tsv
[2023-03-18 10:02:57,801] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:02:57,803] [INFO] DFAST_QC result json was written to OceanDNA-b16280/dqc_result.json
[2023-03-18 10:02:57,803] [INFO] DFAST_QC completed!
[2023-03-18 10:02:57,803] [INFO] Total running time: 0h0m46s