[2023-03-15 15:51:29,975] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:51:29,975] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:51:29,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg44b5784a-303c-4642-a855-69cda795c1c6/dqc_reference
[2023-03-15 15:51:31,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:51:31,681] [INFO] Task started: Prodigal
[2023-03-15 15:51:31,681] [INFO] Running command: cat /var/lib/cwl/stg9ffbbffe-902a-49ed-abe5-dbfb46886483/OceanDNA-b41334.fa | prodigal -d OceanDNA-b41334/cds.fna -a OceanDNA-b41334/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:51:41,563] [INFO] Task succeeded: Prodigal
[2023-03-15 15:51:41,563] [INFO] Task started: HMMsearch
[2023-03-15 15:51:41,563] [INFO] Running command: hmmsearch --tblout OceanDNA-b41334/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44b5784a-303c-4642-a855-69cda795c1c6/dqc_reference/reference_markers.hmm OceanDNA-b41334/protein.faa > /dev/null
[2023-03-15 15:51:41,734] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:51:41,734] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ffbbffe-902a-49ed-abe5-dbfb46886483/OceanDNA-b41334.fa]
[2023-03-15 15:51:41,753] [INFO] Query marker FASTA was written to OceanDNA-b41334/markers.fasta
[2023-03-15 15:51:41,753] [INFO] Task started: Blastn
[2023-03-15 15:51:41,753] [INFO] Running command: blastn -query OceanDNA-b41334/markers.fasta -db /var/lib/cwl/stg44b5784a-303c-4642-a855-69cda795c1c6/dqc_reference/reference_markers.fasta -out OceanDNA-b41334/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:51:42,406] [INFO] Task succeeded: Blastn
[2023-03-15 15:51:42,750] [INFO] Selected 20 target genomes.
[2023-03-15 15:51:42,750] [INFO] Target genome list was writen to OceanDNA-b41334/target_genomes.txt
[2023-03-15 15:51:42,761] [INFO] Task started: fastANI
[2023-03-15 15:51:42,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ffbbffe-902a-49ed-abe5-dbfb46886483/OceanDNA-b41334.fa --refList OceanDNA-b41334/target_genomes.txt --output OceanDNA-b41334/fastani_result.tsv --threads 1
[2023-03-15 15:51:56,892] [INFO] Task succeeded: fastANI
[2023-03-15 15:51:56,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44b5784a-303c-4642-a855-69cda795c1c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:51:56,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44b5784a-303c-4642-a855-69cda795c1c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:51:56,896] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 15:51:56,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 15:51:56,897] [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
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	97.4973	367	375	95	conclusive
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	80.4595	234	375	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	78.7497	89	375	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	78.6772	53	375	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:51:56,897] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41334/tc_result.tsv
[2023-03-15 15:51:56,897] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:51:56,897] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:51:56,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44b5784a-303c-4642-a855-69cda795c1c6/dqc_reference/checkm_data
[2023-03-15 15:51:56,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:51:56,903] [INFO] Task started: CheckM
[2023-03-15 15:51:56,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41334/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41334/checkm_input OceanDNA-b41334/checkm_result
[2023-03-15 15:52:26,919] [INFO] Task succeeded: CheckM
[2023-03-15 15:52:26,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.28%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 15:52:26,922] [INFO] ===== Completeness check finished =====
[2023-03-15 15:52:26,922] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:52:26,922] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41334/markers.fasta)
[2023-03-15 15:52:26,922] [INFO] Task started: Blastn
[2023-03-15 15:52:26,922] [INFO] Running command: blastn -query OceanDNA-b41334/markers.fasta -db /var/lib/cwl/stg44b5784a-303c-4642-a855-69cda795c1c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41334/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:52:27,929] [INFO] Task succeeded: Blastn
[2023-03-15 15:52:27,930] [INFO] Selected 16 target genomes.
[2023-03-15 15:52:27,930] [INFO] Target genome list was writen to OceanDNA-b41334/target_genomes_gtdb.txt
[2023-03-15 15:52:27,949] [INFO] Task started: fastANI
[2023-03-15 15:52:27,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ffbbffe-902a-49ed-abe5-dbfb46886483/OceanDNA-b41334.fa --refList OceanDNA-b41334/target_genomes_gtdb.txt --output OceanDNA-b41334/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:52:38,242] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:38,248] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:52:38,248] [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_000422845.1	s__Oceanobacter kriegii	97.4973	367	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002723385.1	s__Oceanobacter sp002723385	78.7479	78	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	99.82	99.82	0.84	0.84	2	-
GCA_002724925.1	s__Oleibacter sp002724925	78.478	52	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.64	97.85	0.94	0.89	5	-
GCF_007785795.1	s__UBA2009 sp002335285	78.4606	83	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_002733205.1	s__UBA2009 sp002733205	78.3948	76	375	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	78.2408	86	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCA_016132445.1	s__UBA2009 sp016132445	78.2208	89	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCA_002298335.1	s__Oleibacter sp002298335	77.8531	76	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	99.94	99.90	0.96	0.95	5	-
--------------------------------------------------------------------------------
[2023-03-15 15:52:38,248] [INFO] GTDB search result was written to OceanDNA-b41334/result_gtdb.tsv
[2023-03-15 15:52:38,249] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:52:38,249] [INFO] DFAST_QC result json was written to OceanDNA-b41334/dqc_result.json
[2023-03-15 15:52:38,250] [INFO] DFAST_QC completed!
[2023-03-15 15:52:38,250] [INFO] Total running time: 0h1m8s