[2023-03-18 01:59:39,744] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,744] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d4bfa1c-897b-4ca1-9f08-54d7c614f876/dqc_reference
[2023-03-18 01:59:40,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,952] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,953] [INFO] Running command: cat /var/lib/cwl/stg9de3d37e-264c-4c9b-a580-f19efe0f3d00/OceanDNA-b23054.fa | prodigal -d OceanDNA-b23054/cds.fna -a OceanDNA-b23054/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:00:01,199] [INFO] Task succeeded: Prodigal
[2023-03-18 02:00:01,200] [INFO] Task started: HMMsearch
[2023-03-18 02:00:01,200] [INFO] Running command: hmmsearch --tblout OceanDNA-b23054/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d4bfa1c-897b-4ca1-9f08-54d7c614f876/dqc_reference/reference_markers.hmm OceanDNA-b23054/protein.faa > /dev/null
[2023-03-18 02:00:01,397] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:00:01,398] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9de3d37e-264c-4c9b-a580-f19efe0f3d00/OceanDNA-b23054.fa]
[2023-03-18 02:00:01,434] [INFO] Query marker FASTA was written to OceanDNA-b23054/markers.fasta
[2023-03-18 02:00:01,435] [INFO] Task started: Blastn
[2023-03-18 02:00:01,435] [INFO] Running command: blastn -query OceanDNA-b23054/markers.fasta -db /var/lib/cwl/stg2d4bfa1c-897b-4ca1-9f08-54d7c614f876/dqc_reference/reference_markers.fasta -out OceanDNA-b23054/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:02,064] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:02,069] [INFO] Selected 24 target genomes.
[2023-03-18 02:00:02,069] [INFO] Target genome list was writen to OceanDNA-b23054/target_genomes.txt
[2023-03-18 02:00:02,081] [INFO] Task started: fastANI
[2023-03-18 02:00:02,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg9de3d37e-264c-4c9b-a580-f19efe0f3d00/OceanDNA-b23054.fa --refList OceanDNA-b23054/target_genomes.txt --output OceanDNA-b23054/fastani_result.tsv --threads 1
[2023-03-18 02:00:20,395] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:20,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d4bfa1c-897b-4ca1-9f08-54d7c614f876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:00:20,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d4bfa1c-897b-4ca1-9f08-54d7c614f876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:00:20,403] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:00:20,403] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:00:20,403] [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
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.1636	87	698	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.1636	87	698	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.1617	53	698	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.1477	54	698	95	below_threshold
Pseudonocardia endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	74.8559	58	698	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	74.8316	79	698	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	74.7721	58	698	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	74.7677	59	698	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	74.6939	61	698	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:00:20,407] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23054/tc_result.tsv
[2023-03-18 02:00:20,414] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:00:20,414] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:00:20,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d4bfa1c-897b-4ca1-9f08-54d7c614f876/dqc_reference/checkm_data
[2023-03-18 02:00:20,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:00:20,443] [INFO] Task started: CheckM
[2023-03-18 02:00:20,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23054/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23054/checkm_input OceanDNA-b23054/checkm_result
[2023-03-18 02:01:03,870] [INFO] Task succeeded: CheckM
[2023-03-18 02:01:03,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 02:01:03,944] [INFO] ===== Completeness check finished =====
[2023-03-18 02:01:03,945] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:01:03,945] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23054/markers.fasta)
[2023-03-18 02:01:03,946] [INFO] Task started: Blastn
[2023-03-18 02:01:03,946] [INFO] Running command: blastn -query OceanDNA-b23054/markers.fasta -db /var/lib/cwl/stg2d4bfa1c-897b-4ca1-9f08-54d7c614f876/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23054/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:01:04,967] [INFO] Task succeeded: Blastn
[2023-03-18 02:01:04,978] [INFO] Selected 23 target genomes.
[2023-03-18 02:01:04,978] [INFO] Target genome list was writen to OceanDNA-b23054/target_genomes_gtdb.txt
[2023-03-18 02:01:05,025] [INFO] Task started: fastANI
[2023-03-18 02:01:05,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg9de3d37e-264c-4c9b-a580-f19efe0f3d00/OceanDNA-b23054.fa --refList OceanDNA-b23054/target_genomes_gtdb.txt --output OceanDNA-b23054/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:01:19,251] [INFO] Task succeeded: fastANI
[2023-03-18 02:01:19,257] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:01:19,257] [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_002705055.1	s__GCA-2705055 sp002705055	83.6052	598	698	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__UBA1135;g__GCA-2705055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382465.1	s__J029 sp014382465	77.1051	135	698	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__UBA1135;g__J029	95.0	98.67	98.67	0.72	0.72	2	-
GCA_003696625.1	s__J029 sp003696625	76.8602	141	698	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__UBA1135;g__J029	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295085.1	s__SHNF01 sp004295085	76.0215	121	698	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__UBA1135;g__SHNF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382805.1	s__JACNIZ01 sp014382805	75.8453	56	698	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__UBA1135;g__JACNIZ01	95.0	95.33	95.33	0.85	0.85	2	-
GCA_007750655.1	s__Pla163 sp007750655	75.821	81	698	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795325.1	s__WYBT01 sp016795325	75.7253	78	698	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525785.1	s__WYBT01 sp011525785	75.5199	99	698	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	75.1326	71	698	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:01:19,260] [INFO] GTDB search result was written to OceanDNA-b23054/result_gtdb.tsv
[2023-03-18 02:01:19,266] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:01:19,271] [INFO] DFAST_QC result json was written to OceanDNA-b23054/dqc_result.json
[2023-03-18 02:01:19,271] [INFO] DFAST_QC completed!
[2023-03-18 02:01:19,271] [INFO] Total running time: 0h1m40s