[2023-03-15 17:50:52,701] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:50:52,701] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:50:52,701] [INFO] DQC Reference Directory: /var/lib/cwl/stge04d0314-ae73-45b8-9095-e0b86930a5df/dqc_reference
[2023-03-15 17:50:53,783] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:50:53,783] [INFO] Task started: Prodigal
[2023-03-15 17:50:53,784] [INFO] Running command: cat /var/lib/cwl/stge24fe19f-dd5f-4b42-b6f2-c91f85a8adb6/OceanDNA-b31655.fa | prodigal -d OceanDNA-b31655/cds.fna -a OceanDNA-b31655/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:51:01,524] [INFO] Task succeeded: Prodigal
[2023-03-15 17:51:01,524] [INFO] Task started: HMMsearch
[2023-03-15 17:51:01,525] [INFO] Running command: hmmsearch --tblout OceanDNA-b31655/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge04d0314-ae73-45b8-9095-e0b86930a5df/dqc_reference/reference_markers.hmm OceanDNA-b31655/protein.faa > /dev/null
[2023-03-15 17:51:01,658] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:51:01,658] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge24fe19f-dd5f-4b42-b6f2-c91f85a8adb6/OceanDNA-b31655.fa]
[2023-03-15 17:51:01,669] [INFO] Query marker FASTA was written to OceanDNA-b31655/markers.fasta
[2023-03-15 17:51:01,670] [INFO] Task started: Blastn
[2023-03-15 17:51:01,670] [INFO] Running command: blastn -query OceanDNA-b31655/markers.fasta -db /var/lib/cwl/stge04d0314-ae73-45b8-9095-e0b86930a5df/dqc_reference/reference_markers.fasta -out OceanDNA-b31655/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:51:02,169] [INFO] Task succeeded: Blastn
[2023-03-15 17:51:02,170] [INFO] Selected 15 target genomes.
[2023-03-15 17:51:02,170] [INFO] Target genome list was writen to OceanDNA-b31655/target_genomes.txt
[2023-03-15 17:51:02,179] [INFO] Task started: fastANI
[2023-03-15 17:51:02,179] [INFO] Running command: fastANI --query /var/lib/cwl/stge24fe19f-dd5f-4b42-b6f2-c91f85a8adb6/OceanDNA-b31655.fa --refList OceanDNA-b31655/target_genomes.txt --output OceanDNA-b31655/fastani_result.tsv --threads 1
[2023-03-15 17:51:09,889] [INFO] Task succeeded: fastANI
[2023-03-15 17:51:09,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge04d0314-ae73-45b8-9095-e0b86930a5df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:51:09,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge04d0314-ae73-45b8-9095-e0b86930a5df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:51:09,899] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:51:09,899] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:51:09,899] [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
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	77.9943	176	419	95	below_threshold
Croceicoccus pelagius	strain=CGMCC 1.15358	GCA_014642495.1	1703341	1703341	type	True	77.9059	169	419	95	below_threshold
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	77.882	164	419	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	77.8578	171	419	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	77.8502	172	419	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	77.5314	141	419	95	below_threshold
Croceicoccus mobilis	strain=Ery22	GCA_001661965.1	1703339	1703339	type	True	77.5312	143	419	95	below_threshold
Croceicoccus mobilis	strain=CGMCC 1.15360	GCA_014642595.1	1703339	1703339	type	True	77.4975	142	419	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.2157	135	419	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	76.9476	139	419	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	76.8915	89	419	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	76.8768	118	419	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	76.7811	115	419	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	76.6484	120	419	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	76.6298	120	419	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:51:09,899] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31655/tc_result.tsv
[2023-03-15 17:51:09,900] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:51:09,900] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:51:09,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge04d0314-ae73-45b8-9095-e0b86930a5df/dqc_reference/checkm_data
[2023-03-15 17:51:09,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:51:09,965] [INFO] Task started: CheckM
[2023-03-15 17:51:09,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31655/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31655/checkm_input OceanDNA-b31655/checkm_result
[2023-03-15 17:51:33,632] [INFO] Task succeeded: CheckM
[2023-03-15 17:51:33,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:51:33,634] [INFO] ===== Completeness check finished =====
[2023-03-15 17:51:33,635] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:51:33,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31655/markers.fasta)
[2023-03-15 17:51:33,636] [INFO] Task started: Blastn
[2023-03-15 17:51:33,636] [INFO] Running command: blastn -query OceanDNA-b31655/markers.fasta -db /var/lib/cwl/stge04d0314-ae73-45b8-9095-e0b86930a5df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31655/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:51:34,206] [INFO] Task succeeded: Blastn
[2023-03-15 17:51:34,207] [INFO] Selected 16 target genomes.
[2023-03-15 17:51:34,207] [INFO] Target genome list was writen to OceanDNA-b31655/target_genomes_gtdb.txt
[2023-03-15 17:51:34,224] [INFO] Task started: fastANI
[2023-03-15 17:51:34,224] [INFO] Running command: fastANI --query /var/lib/cwl/stge24fe19f-dd5f-4b42-b6f2-c91f85a8adb6/OceanDNA-b31655.fa --refList OceanDNA-b31655/target_genomes_gtdb.txt --output OceanDNA-b31655/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:51:42,679] [INFO] Task succeeded: fastANI
[2023-03-15 17:51:42,688] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:51:42,688] [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_007570835.1	s__Croceicoccus sediminis	77.9748	177	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661675.2	s__Croceicoccus marinus	77.9033	163	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	96.65	96.65	0.86	0.86	2	-
GCF_001661915.1	s__Croceicoccus pelagius	77.8578	171	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018398395.1	s__Croceicoccus sp018398395	77.8502	172	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	77.5314	141	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661965.1	s__Croceicoccus mobilis	77.5312	143	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014652615.1	s__Novosphingobium arvoryzae	77.2157	135	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	77.1941	136	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004364785.1	s__Novosphingobium sp004364785	77.0394	114	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	77.0047	125	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	76.9476	139	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	76.8593	119	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	76.7811	115	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	76.6529	114	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018491765.1	s__Novosphingobium profundi	76.6309	121	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	76.2938	91	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:51:42,689] [INFO] GTDB search result was written to OceanDNA-b31655/result_gtdb.tsv
[2023-03-15 17:51:42,689] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:51:42,690] [INFO] DFAST_QC result json was written to OceanDNA-b31655/dqc_result.json
[2023-03-15 17:51:42,691] [INFO] DFAST_QC completed!
[2023-03-15 17:51:42,691] [INFO] Total running time: 0h0m50s