[2023-03-15 12:33:51,708] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,708] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg89375a2e-9e51-4a26-9c8a-c1df1cd4a621/dqc_reference
[2023-03-15 12:33:52,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,826] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,826] [INFO] Running command: cat /var/lib/cwl/stge6012d47-d033-4f0e-aa1f-7a4a908f3074/OceanDNA-b20819.fa | prodigal -d OceanDNA-b20819/cds.fna -a OceanDNA-b20819/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:07,375] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:07,376] [INFO] Task started: HMMsearch
[2023-03-15 12:34:07,376] [INFO] Running command: hmmsearch --tblout OceanDNA-b20819/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89375a2e-9e51-4a26-9c8a-c1df1cd4a621/dqc_reference/reference_markers.hmm OceanDNA-b20819/protein.faa > /dev/null
[2023-03-15 12:34:07,568] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:07,568] [INFO] Found 6/6 markers.
[2023-03-15 12:34:07,588] [INFO] Query marker FASTA was written to OceanDNA-b20819/markers.fasta
[2023-03-15 12:34:07,588] [INFO] Task started: Blastn
[2023-03-15 12:34:07,588] [INFO] Running command: blastn -query OceanDNA-b20819/markers.fasta -db /var/lib/cwl/stg89375a2e-9e51-4a26-9c8a-c1df1cd4a621/dqc_reference/reference_markers.fasta -out OceanDNA-b20819/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:08,155] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:08,156] [INFO] Selected 18 target genomes.
[2023-03-15 12:34:08,156] [INFO] Target genome list was writen to OceanDNA-b20819/target_genomes.txt
[2023-03-15 12:34:08,168] [INFO] Task started: fastANI
[2023-03-15 12:34:08,168] [INFO] Running command: fastANI --query /var/lib/cwl/stge6012d47-d033-4f0e-aa1f-7a4a908f3074/OceanDNA-b20819.fa --refList OceanDNA-b20819/target_genomes.txt --output OceanDNA-b20819/fastani_result.tsv --threads 1
[2023-03-15 12:34:16,056] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:16,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89375a2e-9e51-4a26-9c8a-c1df1cd4a621/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:16,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89375a2e-9e51-4a26-9c8a-c1df1cd4a621/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:16,057] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:16,057] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:34:16,057] [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 12:34:16,058] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20819/tc_result.tsv
[2023-03-15 12:34:16,059] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:16,059] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:16,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89375a2e-9e51-4a26-9c8a-c1df1cd4a621/dqc_reference/checkm_data
[2023-03-15 12:34:16,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:16,068] [INFO] Task started: CheckM
[2023-03-15 12:34:16,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20819/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20819/checkm_input OceanDNA-b20819/checkm_result
[2023-03-15 12:34:55,994] [INFO] Task succeeded: CheckM
[2023-03-15 12:34:55,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:34:56,010] [INFO] ===== Completeness check finished =====
[2023-03-15 12:34:56,010] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:34:56,010] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20819/markers.fasta)
[2023-03-15 12:34:56,011] [INFO] Task started: Blastn
[2023-03-15 12:34:56,011] [INFO] Running command: blastn -query OceanDNA-b20819/markers.fasta -db /var/lib/cwl/stg89375a2e-9e51-4a26-9c8a-c1df1cd4a621/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20819/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:56,970] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:56,975] [INFO] Selected 16 target genomes.
[2023-03-15 12:34:56,975] [INFO] Target genome list was writen to OceanDNA-b20819/target_genomes_gtdb.txt
[2023-03-15 12:34:57,118] [INFO] Task started: fastANI
[2023-03-15 12:34:57,118] [INFO] Running command: fastANI --query /var/lib/cwl/stge6012d47-d033-4f0e-aa1f-7a4a908f3074/OceanDNA-b20819.fa --refList OceanDNA-b20819/target_genomes_gtdb.txt --output OceanDNA-b20819/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:35:04,399] [INFO] Task succeeded: fastANI
[2023-03-15 12:35:04,405] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:35:04,405] [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_013202385.1	s__JABMPR01 sp013202385	80.8033	439	861	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650795.1	s__JABMPR01 sp018650795	77.1495	173	861	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.79	99.56	0.89	0.81	14	-
GCA_016844945.1	s__JABMPR01 sp016844945	77.1303	155	861	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845065.1	s__JABMPR01 sp016845065	77.0374	163	861	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673925.1	s__JABMPR01 sp018673925	77.0135	188	861	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.95	99.91	0.96	0.94	16	-
GCA_016844955.1	s__JABMPR01 sp016844955	76.9722	190	861	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650445.1	s__JABMPR01 sp018650445	76.8787	164	861	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.76	99.61	0.86	0.82	5	-
GCA_016784545.1	s__JABMPR01 sp016784545	76.8676	178	861	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:35:04,406] [INFO] GTDB search result was written to OceanDNA-b20819/result_gtdb.tsv
[2023-03-15 12:35:04,408] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:35:04,411] [INFO] DFAST_QC result json was written to OceanDNA-b20819/dqc_result.json
[2023-03-15 12:35:04,411] [INFO] DFAST_QC completed!
[2023-03-15 12:35:04,411] [INFO] Total running time: 0h1m13s