[2023-03-15 23:07:02,632] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,632] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg600834f9-1db9-4513-aab0-0d65be3b250c/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,966] [INFO] Running command: cat /var/lib/cwl/stgebb00bcf-eed2-436e-a7aa-37d32c4a037d/OceanDNA-b22817.fa | prodigal -d OceanDNA-b22817/cds.fna -a OceanDNA-b22817/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:34,020] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:34,020] [INFO] Task started: HMMsearch
[2023-03-15 23:07:34,020] [INFO] Running command: hmmsearch --tblout OceanDNA-b22817/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg600834f9-1db9-4513-aab0-0d65be3b250c/dqc_reference/reference_markers.hmm OceanDNA-b22817/protein.faa > /dev/null
[2023-03-15 23:07:34,311] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:34,312] [INFO] Found 6/6 markers.
[2023-03-15 23:07:34,343] [INFO] Query marker FASTA was written to OceanDNA-b22817/markers.fasta
[2023-03-15 23:07:34,344] [INFO] Task started: Blastn
[2023-03-15 23:07:34,344] [INFO] Running command: blastn -query OceanDNA-b22817/markers.fasta -db /var/lib/cwl/stg600834f9-1db9-4513-aab0-0d65be3b250c/dqc_reference/reference_markers.fasta -out OceanDNA-b22817/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:34,902] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:34,902] [INFO] Selected 32 target genomes.
[2023-03-15 23:07:34,903] [INFO] Target genome list was writen to OceanDNA-b22817/target_genomes.txt
[2023-03-15 23:07:34,939] [INFO] Task started: fastANI
[2023-03-15 23:07:34,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb00bcf-eed2-436e-a7aa-37d32c4a037d/OceanDNA-b22817.fa --refList OceanDNA-b22817/target_genomes.txt --output OceanDNA-b22817/fastani_result.tsv --threads 1
[2023-03-15 23:08:02,207] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:02,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg600834f9-1db9-4513-aab0-0d65be3b250c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:08:02,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg600834f9-1db9-4513-aab0-0d65be3b250c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:08:02,212] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:08:02,213] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:08:02,213] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.3307	100	1707	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	75.3208	50	1707	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.779	58	1707	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.7307	54	1707	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:08:02,216] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22817/tc_result.tsv
[2023-03-15 23:08:02,217] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:08:02,217] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:08:02,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg600834f9-1db9-4513-aab0-0d65be3b250c/dqc_reference/checkm_data
[2023-03-15 23:08:02,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:08:02,240] [INFO] Task started: CheckM
[2023-03-15 23:08:02,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22817/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22817/checkm_input OceanDNA-b22817/checkm_result
[2023-03-15 23:09:15,964] [INFO] Task succeeded: CheckM
[2023-03-15 23:09:15,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:09:16,038] [INFO] ===== Completeness check finished =====
[2023-03-15 23:09:16,038] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:09:16,038] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22817/markers.fasta)
[2023-03-15 23:09:16,040] [INFO] Task started: Blastn
[2023-03-15 23:09:16,040] [INFO] Running command: blastn -query OceanDNA-b22817/markers.fasta -db /var/lib/cwl/stg600834f9-1db9-4513-aab0-0d65be3b250c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22817/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:09:16,797] [INFO] Task succeeded: Blastn
[2023-03-15 23:09:16,798] [INFO] Selected 28 target genomes.
[2023-03-15 23:09:16,798] [INFO] Target genome list was writen to OceanDNA-b22817/target_genomes_gtdb.txt
[2023-03-15 23:09:16,871] [INFO] Task started: fastANI
[2023-03-15 23:09:16,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb00bcf-eed2-436e-a7aa-37d32c4a037d/OceanDNA-b22817.fa --refList OceanDNA-b22817/target_genomes_gtdb.txt --output OceanDNA-b22817/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:09:43,913] [INFO] Task succeeded: fastANI
[2023-03-15 23:09:43,920] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:09:43,920] [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_016124895.1	s__JABMPE01 sp016124895	76.327	277	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203845.1	s__JABMPE01 sp013203845	75.9979	245	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872645.1	s__SXKJ01 sp016872645	75.5236	80	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.3382	99	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.3311	58	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445035.1	s__UBA8437 sp003445035	75.2988	67	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	75.1944	81	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCA_005778115.1	s__SXKJ01 sp005778115	75.1817	88	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.84	99.84	0.89	0.89	2	-
GCA_900299185.1	s__AM-0621 sp900299185	75.0976	90	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__AM-0621	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	74.9707	64	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	74.7836	57	1707	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:09:43,928] [INFO] GTDB search result was written to OceanDNA-b22817/result_gtdb.tsv
[2023-03-15 23:09:43,928] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:09:43,929] [INFO] DFAST_QC result json was written to OceanDNA-b22817/dqc_result.json
[2023-03-15 23:09:43,929] [INFO] DFAST_QC completed!
[2023-03-15 23:09:43,929] [INFO] Total running time: 0h2m41s