[2023-03-16 04:31:43,753] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:31:43,753] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:31:43,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg2aca65c0-f090-4465-a33a-86477736eec4/dqc_reference
[2023-03-16 04:31:45,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:31:45,538] [INFO] Task started: Prodigal
[2023-03-16 04:31:45,538] [INFO] Running command: cat /var/lib/cwl/stgda06e561-1eeb-4ff1-8bc8-fd3b7acc014e/OceanDNA-b41349.fa | prodigal -d OceanDNA-b41349/cds.fna -a OceanDNA-b41349/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:32:04,404] [INFO] Task succeeded: Prodigal
[2023-03-16 04:32:04,405] [INFO] Task started: HMMsearch
[2023-03-16 04:32:04,405] [INFO] Running command: hmmsearch --tblout OceanDNA-b41349/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2aca65c0-f090-4465-a33a-86477736eec4/dqc_reference/reference_markers.hmm OceanDNA-b41349/protein.faa > /dev/null
[2023-03-16 04:32:04,851] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:32:04,852] [INFO] Found 6/6 markers.
[2023-03-16 04:32:04,872] [INFO] Query marker FASTA was written to OceanDNA-b41349/markers.fasta
[2023-03-16 04:32:04,872] [INFO] Task started: Blastn
[2023-03-16 04:32:04,872] [INFO] Running command: blastn -query OceanDNA-b41349/markers.fasta -db /var/lib/cwl/stg2aca65c0-f090-4465-a33a-86477736eec4/dqc_reference/reference_markers.fasta -out OceanDNA-b41349/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:32:05,527] [INFO] Task succeeded: Blastn
[2023-03-16 04:32:05,528] [INFO] Selected 24 target genomes.
[2023-03-16 04:32:05,528] [INFO] Target genome list was writen to OceanDNA-b41349/target_genomes.txt
[2023-03-16 04:32:05,544] [INFO] Task started: fastANI
[2023-03-16 04:32:05,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgda06e561-1eeb-4ff1-8bc8-fd3b7acc014e/OceanDNA-b41349.fa --refList OceanDNA-b41349/target_genomes.txt --output OceanDNA-b41349/fastani_result.tsv --threads 1
[2023-03-16 04:32:21,630] [INFO] Task succeeded: fastANI
[2023-03-16 04:32:21,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2aca65c0-f090-4465-a33a-86477736eec4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:32:21,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2aca65c0-f090-4465-a33a-86477736eec4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:32:21,637] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 04:32:21,637] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 04:32:21,637] [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
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	95.047	994	1078	95	conclusive
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	78.4766	243	1078	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	77.9776	150	1078	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.3875	150	1078	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.3025	111	1078	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	75.6884	50	1078	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	75.6884	50	1078	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:32:21,637] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41349/tc_result.tsv
[2023-03-16 04:32:21,637] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:32:21,638] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:32:21,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2aca65c0-f090-4465-a33a-86477736eec4/dqc_reference/checkm_data
[2023-03-16 04:32:21,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:32:21,665] [INFO] Task started: CheckM
[2023-03-16 04:32:21,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41349/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41349/checkm_input OceanDNA-b41349/checkm_result
[2023-03-16 04:33:10,796] [INFO] Task succeeded: CheckM
[2023-03-16 04:33:10,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:33:10,821] [INFO] ===== Completeness check finished =====
[2023-03-16 04:33:10,821] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:33:10,821] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41349/markers.fasta)
[2023-03-16 04:33:10,821] [INFO] Task started: Blastn
[2023-03-16 04:33:10,821] [INFO] Running command: blastn -query OceanDNA-b41349/markers.fasta -db /var/lib/cwl/stg2aca65c0-f090-4465-a33a-86477736eec4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41349/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:33:11,906] [INFO] Task succeeded: Blastn
[2023-03-16 04:33:11,907] [INFO] Selected 10 target genomes.
[2023-03-16 04:33:11,907] [INFO] Target genome list was writen to OceanDNA-b41349/target_genomes_gtdb.txt
[2023-03-16 04:33:11,919] [INFO] Task started: fastANI
[2023-03-16 04:33:11,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgda06e561-1eeb-4ff1-8bc8-fd3b7acc014e/OceanDNA-b41349.fa --refList OceanDNA-b41349/target_genomes_gtdb.txt --output OceanDNA-b41349/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:33:20,579] [INFO] Task succeeded: fastANI
[2023-03-16 04:33:20,585] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 04:33:20,585] [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_002331105.1	s__Oleibacter sp002331105	99.8065	926	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	97.07	0.90	0.84	7	inconclusive
GCF_900156675.1	s__Oleibacter marinus	95.047	994	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	inconclusive
GCA_002724925.1	s__Oleibacter sp002724925	87.8152	934	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.64	97.85	0.94	0.89	5	-
GCA_006212115.1	s__Oleibacter sp006212115	81.472	481	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733205.1	s__UBA2009 sp002733205	78.0859	175	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	96.83	96.83	0.84	0.84	2	-
GCA_002706025.1	s__UBA2009 sp002706025	77.9188	205	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCF_007785795.1	s__UBA2009 sp002335285	77.8671	230	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCF_002237535.1	s__Bacterioplanes sanyensis_A	77.5558	117	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:33:20,585] [INFO] GTDB search result was written to OceanDNA-b41349/result_gtdb.tsv
[2023-03-16 04:33:20,585] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:33:20,586] [INFO] DFAST_QC result json was written to OceanDNA-b41349/dqc_result.json
[2023-03-16 04:33:20,586] [INFO] DFAST_QC completed!
[2023-03-16 04:33:20,587] [INFO] Total running time: 0h1m37s