[2023-03-17 05:01:06,446] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,446] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,446] [INFO] DQC Reference Directory: /var/lib/cwl/stgeace54a0-1407-4f35-88ce-037eea8da342/dqc_reference
[2023-03-17 05:01:07,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:07,999] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,000] [INFO] Running command: cat /var/lib/cwl/stgc17e0800-ef6e-4399-b05b-5f994501e343/OceanDNA-b41418.fa | prodigal -d OceanDNA-b41418/cds.fna -a OceanDNA-b41418/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:28,517] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:28,517] [INFO] Task started: HMMsearch
[2023-03-17 05:01:28,517] [INFO] Running command: hmmsearch --tblout OceanDNA-b41418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeace54a0-1407-4f35-88ce-037eea8da342/dqc_reference/reference_markers.hmm OceanDNA-b41418/protein.faa > /dev/null
[2023-03-17 05:01:28,727] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:28,727] [INFO] Found 6/6 markers.
[2023-03-17 05:01:28,749] [INFO] Query marker FASTA was written to OceanDNA-b41418/markers.fasta
[2023-03-17 05:01:28,749] [INFO] Task started: Blastn
[2023-03-17 05:01:28,749] [INFO] Running command: blastn -query OceanDNA-b41418/markers.fasta -db /var/lib/cwl/stgeace54a0-1407-4f35-88ce-037eea8da342/dqc_reference/reference_markers.fasta -out OceanDNA-b41418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:29,396] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:29,397] [INFO] Selected 27 target genomes.
[2023-03-17 05:01:29,397] [INFO] Target genome list was writen to OceanDNA-b41418/target_genomes.txt
[2023-03-17 05:01:29,409] [INFO] Task started: fastANI
[2023-03-17 05:01:29,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgc17e0800-ef6e-4399-b05b-5f994501e343/OceanDNA-b41418.fa --refList OceanDNA-b41418/target_genomes.txt --output OceanDNA-b41418/fastani_result.tsv --threads 1
[2023-03-17 05:01:46,567] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:46,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeace54a0-1407-4f35-88ce-037eea8da342/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:46,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeace54a0-1407-4f35-88ce-037eea8da342/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:46,572] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 05:01:46,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 05:01:46,573] [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
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	98.2977	1116	1198	95	conclusive
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	78.3715	172	1198	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	77.7359	157	1198	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	77.6443	95	1198	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.6057	92	1198	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:01:46,573] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41418/tc_result.tsv
[2023-03-17 05:01:46,573] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:46,573] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:46,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeace54a0-1407-4f35-88ce-037eea8da342/dqc_reference/checkm_data
[2023-03-17 05:01:46,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:46,579] [INFO] Task started: CheckM
[2023-03-17 05:01:46,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41418/checkm_input OceanDNA-b41418/checkm_result
[2023-03-17 05:02:38,339] [INFO] Task succeeded: CheckM
[2023-03-17 05:02:38,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:02:38,341] [INFO] ===== Completeness check finished =====
[2023-03-17 05:02:38,342] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:02:38,342] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41418/markers.fasta)
[2023-03-17 05:02:38,342] [INFO] Task started: Blastn
[2023-03-17 05:02:38,342] [INFO] Running command: blastn -query OceanDNA-b41418/markers.fasta -db /var/lib/cwl/stgeace54a0-1407-4f35-88ce-037eea8da342/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:02:39,374] [INFO] Task succeeded: Blastn
[2023-03-17 05:02:39,375] [INFO] Selected 20 target genomes.
[2023-03-17 05:02:39,375] [INFO] Target genome list was writen to OceanDNA-b41418/target_genomes_gtdb.txt
[2023-03-17 05:02:39,688] [INFO] Task started: fastANI
[2023-03-17 05:02:39,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgc17e0800-ef6e-4399-b05b-5f994501e343/OceanDNA-b41418.fa --refList OceanDNA-b41418/target_genomes_gtdb.txt --output OceanDNA-b41418/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:02:52,720] [INFO] Task succeeded: fastANI
[2023-03-17 05:02:52,727] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:02:52,727] [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_000355675.1	s__Thalassolituus oleivorans	98.2977	1116	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Thalassolituus	95.0	98.27	98.03	0.89	0.78	10	conclusive
GCA_002733205.1	s__UBA2009 sp002733205	79.134	203	1198	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_002724925.1	s__Oleibacter sp002724925	78.3011	154	1198	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_002733645.1	s__Oleibacter sp002733645	78.1932	231	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	97.97	97.97	0.87	0.87	2	-
GCF_007785795.1	s__UBA2009 sp002335285	77.9136	212	1198	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_002331105.1	s__Oleibacter sp002331105	77.7377	132	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	97.07	0.90	0.84	7	-
GCA_014859445.1	s__Bacterioplanes sp014859445	77.7365	130	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298335.1	s__Oleibacter sp002298335	77.6463	114	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	99.94	99.90	0.96	0.95	5	-
GCA_002314145.1	s__UBA2009 sp002314145	77.4911	141	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCF_002237535.1	s__Bacterioplanes sanyensis_A	77.3891	116	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212115.1	s__Oleibacter sp006212115	76.8504	113	1198	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_000967895.1	s__Oleispira antarctica	76.6293	100	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	99.07	99.06	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2023-03-17 05:02:52,727] [INFO] GTDB search result was written to OceanDNA-b41418/result_gtdb.tsv
[2023-03-17 05:02:52,728] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:02:52,729] [INFO] DFAST_QC result json was written to OceanDNA-b41418/dqc_result.json
[2023-03-17 05:02:52,729] [INFO] DFAST_QC completed!
[2023-03-17 05:02:52,729] [INFO] Total running time: 0h1m46s