[2023-03-16 18:28:42,328] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:28:42,329] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:28:42,329] [INFO] DQC Reference Directory: /var/lib/cwl/stg98589f12-c63e-4ee7-8deb-5afa98806f85/dqc_reference
[2023-03-16 18:28:43,431] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:28:43,432] [INFO] Task started: Prodigal
[2023-03-16 18:28:43,432] [INFO] Running command: cat /var/lib/cwl/stg80a23bab-1279-41e2-9ccc-87881f5eb897/OceanDNA-b34938.fa | prodigal -d OceanDNA-b34938/cds.fna -a OceanDNA-b34938/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:29:17,718] [INFO] Task succeeded: Prodigal
[2023-03-16 18:29:17,719] [INFO] Task started: HMMsearch
[2023-03-16 18:29:17,719] [INFO] Running command: hmmsearch --tblout OceanDNA-b34938/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98589f12-c63e-4ee7-8deb-5afa98806f85/dqc_reference/reference_markers.hmm OceanDNA-b34938/protein.faa > /dev/null
[2023-03-16 18:29:18,252] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:29:18,252] [INFO] Found 6/6 markers.
[2023-03-16 18:29:18,294] [INFO] Query marker FASTA was written to OceanDNA-b34938/markers.fasta
[2023-03-16 18:29:18,307] [INFO] Task started: Blastn
[2023-03-16 18:29:18,308] [INFO] Running command: blastn -query OceanDNA-b34938/markers.fasta -db /var/lib/cwl/stg98589f12-c63e-4ee7-8deb-5afa98806f85/dqc_reference/reference_markers.fasta -out OceanDNA-b34938/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:29:20,259] [INFO] Task succeeded: Blastn
[2023-03-16 18:29:20,262] [INFO] Selected 12 target genomes.
[2023-03-16 18:29:20,262] [INFO] Target genome list was writen to OceanDNA-b34938/target_genomes.txt
[2023-03-16 18:29:20,268] [INFO] Task started: fastANI
[2023-03-16 18:29:20,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg80a23bab-1279-41e2-9ccc-87881f5eb897/OceanDNA-b34938.fa --refList OceanDNA-b34938/target_genomes.txt --output OceanDNA-b34938/fastani_result.tsv --threads 1
[2023-03-16 18:29:34,693] [INFO] Task succeeded: fastANI
[2023-03-16 18:29:34,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98589f12-c63e-4ee7-8deb-5afa98806f85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:29:34,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98589f12-c63e-4ee7-8deb-5afa98806f85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:29:34,702] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:29:34,702] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:29:34,702] [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
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	88.3127	1124	1451	95	below_threshold
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	78.593	485	1451	95	below_threshold
Rheinheimera tangshanensis	strain=JA3-B52	GCA_008017875.1	400153	400153	type	True	78.2767	310	1451	95	below_threshold
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	78.2686	308	1451	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	78.2651	301	1451	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	78.0508	281	1451	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	77.5069	229	1451	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	77.392	217	1451	95	below_threshold
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	77.3804	193	1451	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	77.1966	189	1451	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	77.0261	230	1451	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	76.9994	103	1451	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:29:34,702] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34938/tc_result.tsv
[2023-03-16 18:29:34,703] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:29:34,703] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:29:34,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98589f12-c63e-4ee7-8deb-5afa98806f85/dqc_reference/checkm_data
[2023-03-16 18:29:34,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:29:34,772] [INFO] Task started: CheckM
[2023-03-16 18:29:34,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34938/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34938/checkm_input OceanDNA-b34938/checkm_result
[2023-03-16 18:30:43,767] [INFO] Task succeeded: CheckM
[2023-03-16 18:30:43,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:30:43,770] [INFO] ===== Completeness check finished =====
[2023-03-16 18:30:43,770] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:30:43,770] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34938/markers.fasta)
[2023-03-16 18:30:43,772] [INFO] Task started: Blastn
[2023-03-16 18:30:43,772] [INFO] Running command: blastn -query OceanDNA-b34938/markers.fasta -db /var/lib/cwl/stg98589f12-c63e-4ee7-8deb-5afa98806f85/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34938/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:30:44,928] [INFO] Task succeeded: Blastn
[2023-03-16 18:30:44,929] [INFO] Selected 8 target genomes.
[2023-03-16 18:30:44,929] [INFO] Target genome list was writen to OceanDNA-b34938/target_genomes_gtdb.txt
[2023-03-16 18:30:44,950] [INFO] Task started: fastANI
[2023-03-16 18:30:44,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg80a23bab-1279-41e2-9ccc-87881f5eb897/OceanDNA-b34938.fa --refList OceanDNA-b34938/target_genomes_gtdb.txt --output OceanDNA-b34938/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:30:52,167] [INFO] Task succeeded: fastANI
[2023-03-16 18:30:52,172] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:30:52,173] [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
GCF_004005945.1	s__Pararheinheimera riviphila	88.3371	1122	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001669775.1	s__Pararheinheimera sp001669775	87.2958	1164	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820995.1	s__Pararheinheimera sp018820995	81.8331	646	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.83	98.80	0.82	0.81	5	-
GCA_003543135.1	s__Pararheinheimera sp003543135	80.3971	660	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.83	98.83	0.95	0.95	2	-
GCF_000711985.1	s__Pararheinheimera texasensis	78.6018	484	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008015325.1	s__Pararheinheimera sp008015325	78.3737	433	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217935.1	s__Pararheinheimera sp000217935	78.2551	311	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018815765.1	s__Pararheinheimera sp018815765	77.7683	274	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:30:52,173] [INFO] GTDB search result was written to OceanDNA-b34938/result_gtdb.tsv
[2023-03-16 18:30:52,173] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:30:52,174] [INFO] DFAST_QC result json was written to OceanDNA-b34938/dqc_result.json
[2023-03-16 18:30:52,174] [INFO] DFAST_QC completed!
[2023-03-16 18:30:52,174] [INFO] Total running time: 0h2m10s