[2023-03-15 21:01:44,346] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,346] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,346] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b35c3eb-d909-4e86-91fb-e2eeb8d50d0c/dqc_reference
[2023-03-15 21:01:45,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,702] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,702] [INFO] Running command: cat /var/lib/cwl/stgea3c582e-c6a8-475b-a925-3517aa96ac77/OceanDNA-b40442.fa | prodigal -d OceanDNA-b40442/cds.fna -a OceanDNA-b40442/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:08,665] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:08,665] [INFO] Task started: HMMsearch
[2023-03-15 21:02:08,665] [INFO] Running command: hmmsearch --tblout OceanDNA-b40442/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b35c3eb-d909-4e86-91fb-e2eeb8d50d0c/dqc_reference/reference_markers.hmm OceanDNA-b40442/protein.faa > /dev/null
[2023-03-15 21:02:08,862] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:08,862] [INFO] Found 6/6 markers.
[2023-03-15 21:02:08,884] [INFO] Query marker FASTA was written to OceanDNA-b40442/markers.fasta
[2023-03-15 21:02:08,884] [INFO] Task started: Blastn
[2023-03-15 21:02:08,884] [INFO] Running command: blastn -query OceanDNA-b40442/markers.fasta -db /var/lib/cwl/stg5b35c3eb-d909-4e86-91fb-e2eeb8d50d0c/dqc_reference/reference_markers.fasta -out OceanDNA-b40442/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:09,578] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:09,579] [INFO] Selected 27 target genomes.
[2023-03-15 21:02:09,579] [INFO] Target genome list was writen to OceanDNA-b40442/target_genomes.txt
[2023-03-15 21:02:09,594] [INFO] Task started: fastANI
[2023-03-15 21:02:09,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgea3c582e-c6a8-475b-a925-3517aa96ac77/OceanDNA-b40442.fa --refList OceanDNA-b40442/target_genomes.txt --output OceanDNA-b40442/fastani_result.tsv --threads 1
[2023-03-15 21:02:27,331] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:27,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b35c3eb-d909-4e86-91fb-e2eeb8d50d0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:27,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b35c3eb-d909-4e86-91fb-e2eeb8d50d0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:27,344] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:27,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:27,344] [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
Pseudohongiella acticola	strain=KCTC 42131	GCA_001758195.1	1524254	1524254	type	True	80.7782	710	1197	95	below_threshold
Pseudohongiella nitratireducens	strain=SCS-49	GCA_001642735.1	1768907	1768907	type	True	77.6111	175	1197	95	below_threshold
Pseudohongiella nitratireducens	strain=CGMCC 1.15425	GCA_014642795.1	1768907	1768907	type	True	77.5584	181	1197	95	below_threshold
Pseudohongiella spirulinae	strain=KCTC 32221	GCA_001444425.1	1249552	1249552	type	True	77.5272	270	1197	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.3638	61	1197	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.9879	76	1197	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	75.9867	61	1197	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	75.9832	59	1197	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	75.9432	73	1197	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	75.9421	73	1197	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	75.9384	53	1197	95	below_threshold
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	75.896	58	1197	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	75.8685	61	1197	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	75.8685	75	1197	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	75.8684	75	1197	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.8489	69	1197	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	75.8192	73	1197	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	75.8073	59	1197	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.7632	52	1197	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	75.6902	68	1197	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	75.6361	53	1197	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:27,344] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40442/tc_result.tsv
[2023-03-15 21:02:27,344] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:27,344] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:27,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b35c3eb-d909-4e86-91fb-e2eeb8d50d0c/dqc_reference/checkm_data
[2023-03-15 21:02:27,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:27,350] [INFO] Task started: CheckM
[2023-03-15 21:02:27,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40442/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40442/checkm_input OceanDNA-b40442/checkm_result
[2023-03-15 21:03:24,733] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:24,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:24,736] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:24,736] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:24,736] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40442/markers.fasta)
[2023-03-15 21:03:24,737] [INFO] Task started: Blastn
[2023-03-15 21:03:24,737] [INFO] Running command: blastn -query OceanDNA-b40442/markers.fasta -db /var/lib/cwl/stg5b35c3eb-d909-4e86-91fb-e2eeb8d50d0c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40442/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:25,931] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:25,932] [INFO] Selected 14 target genomes.
[2023-03-15 21:03:25,932] [INFO] Target genome list was writen to OceanDNA-b40442/target_genomes_gtdb.txt
[2023-03-15 21:03:26,367] [INFO] Task started: fastANI
[2023-03-15 21:03:26,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgea3c582e-c6a8-475b-a925-3517aa96ac77/OceanDNA-b40442.fa --refList OceanDNA-b40442/target_genomes_gtdb.txt --output OceanDNA-b40442/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:35,919] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:35,926] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:03:35,927] [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_002711845.1	s__Pseudohongiella sp002711845	85.83	941	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_011050365.1	s__Pseudohongiella sp011050365	81.8835	829	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001758195.1	s__Pseudohongiella acticola	80.7784	710	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354805.1	s__Pseudohongiella sp002354805	77.6874	287	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.49	99.10	0.99	0.98	3	-
GCA_002706685.1	s__Pseudohongiella sp002706685	77.5904	302	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.93	99.90	0.98	0.96	5	-
GCF_001444425.1	s__Pseudohongiella spirulinae	77.5162	271	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004535785.1	s__Pseudohongiella sp004535785	77.2987	210	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001802565.1	s__UBA5078 sp001802565	77.2407	136	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862645.1	s__UBA5078 sp903862645	76.5329	97	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002416505.1	s__UBA5078 sp002416505	76.2422	87	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000497835.1	s__Pseudomonas_E sp000497835	75.8152	69	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	75.6743	69	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:35,927] [INFO] GTDB search result was written to OceanDNA-b40442/result_gtdb.tsv
[2023-03-15 21:03:35,927] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:35,929] [INFO] DFAST_QC result json was written to OceanDNA-b40442/dqc_result.json
[2023-03-15 21:03:35,929] [INFO] DFAST_QC completed!
[2023-03-15 21:03:35,929] [INFO] Total running time: 0h1m52s