[2023-03-15 07:52:40,309] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,309] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,309] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd0d3d68-047e-4166-afa6-85d736c73ef7/dqc_reference
[2023-03-15 07:52:41,454] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,455] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,455] [INFO] Running command: cat /var/lib/cwl/stg3bbe4d64-23b2-4567-9c86-adb0b9da7552/OceanDNA-b4937.fa | prodigal -d OceanDNA-b4937/cds.fna -a OceanDNA-b4937/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:45,675] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:45,675] [INFO] Task started: HMMsearch
[2023-03-15 07:52:45,675] [INFO] Running command: hmmsearch --tblout OceanDNA-b4937/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd0d3d68-047e-4166-afa6-85d736c73ef7/dqc_reference/reference_markers.hmm OceanDNA-b4937/protein.faa > /dev/null
[2023-03-15 07:52:45,854] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:45,855] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3bbe4d64-23b2-4567-9c86-adb0b9da7552/OceanDNA-b4937.fa]
[2023-03-15 07:52:45,862] [INFO] Query marker FASTA was written to OceanDNA-b4937/markers.fasta
[2023-03-15 07:52:45,862] [INFO] Task started: Blastn
[2023-03-15 07:52:45,862] [INFO] Running command: blastn -query OceanDNA-b4937/markers.fasta -db /var/lib/cwl/stgdd0d3d68-047e-4166-afa6-85d736c73ef7/dqc_reference/reference_markers.fasta -out OceanDNA-b4937/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:46,417] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:46,417] [INFO] Selected 24 target genomes.
[2023-03-15 07:52:46,418] [INFO] Target genome list was writen to OceanDNA-b4937/target_genomes.txt
[2023-03-15 07:52:46,429] [INFO] Task started: fastANI
[2023-03-15 07:52:46,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbe4d64-23b2-4567-9c86-adb0b9da7552/OceanDNA-b4937.fa --refList OceanDNA-b4937/target_genomes.txt --output OceanDNA-b4937/fastani_result.tsv --threads 1
[2023-03-15 07:53:03,031] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:03,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd0d3d68-047e-4166-afa6-85d736c73ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:03,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd0d3d68-047e-4166-afa6-85d736c73ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:03,032] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:53:03,032] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:53:03,032] [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 07:53:03,032] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4937/tc_result.tsv
[2023-03-15 07:53:03,033] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:03,033] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:03,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd0d3d68-047e-4166-afa6-85d736c73ef7/dqc_reference/checkm_data
[2023-03-15 07:53:03,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:03,038] [INFO] Task started: CheckM
[2023-03-15 07:53:03,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4937/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4937/checkm_input OceanDNA-b4937/checkm_result
[2023-03-15 07:53:20,677] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:20,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 8.33%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:20,679] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:20,679] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:20,680] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4937/markers.fasta)
[2023-03-15 07:53:20,680] [INFO] Task started: Blastn
[2023-03-15 07:53:20,680] [INFO] Running command: blastn -query OceanDNA-b4937/markers.fasta -db /var/lib/cwl/stgdd0d3d68-047e-4166-afa6-85d736c73ef7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4937/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:21,566] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:21,567] [INFO] Selected 15 target genomes.
[2023-03-15 07:53:21,567] [INFO] Target genome list was writen to OceanDNA-b4937/target_genomes_gtdb.txt
[2023-03-15 07:53:21,624] [INFO] Task started: fastANI
[2023-03-15 07:53:21,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbe4d64-23b2-4567-9c86-adb0b9da7552/OceanDNA-b4937.fa --refList OceanDNA-b4937/target_genomes_gtdb.txt --output OceanDNA-b4937/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:53:25,551] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:25,558] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:53:25,558] [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_018695965.1	s__GCA-002697625 sp018695965	88.9491	171	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	98.45	97.65	0.78	0.72	6	-
GCA_002710495.1	s__GCA-002697625 sp002710495	87.4279	183	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514225.1	s__GCA-002697625 sp902514225	82.8776	105	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647945.1	s__GCA-002697625 sp018647945	79.523	136	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	99.64	99.58	0.90	0.90	3	-
GCA_905478555.1	s__GCA-002697625 sp905478555	78.9529	137	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
GCA_002697625.1	s__GCA-002697625 sp002697625	78.528	116	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	78.047	70	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	77.8785	72	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_905479165.1	s__UWMA-0277 sp905479165	77.4243	56	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696275.1	s__GCA-002697625 sp002696275	77.4199	95	223	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:53:25,558] [INFO] GTDB search result was written to OceanDNA-b4937/result_gtdb.tsv
[2023-03-15 07:53:25,558] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:53:25,559] [INFO] DFAST_QC result json was written to OceanDNA-b4937/dqc_result.json
[2023-03-15 07:53:25,559] [INFO] DFAST_QC completed!
[2023-03-15 07:53:25,559] [INFO] Total running time: 0h0m45s