[2023-03-17 11:13:09,866] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:13:09,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:13:09,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgdda84dea-06c1-4b2c-a0af-7a41255d3f56/dqc_reference
[2023-03-17 11:13:10,998] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:13:10,999] [INFO] Task started: Prodigal
[2023-03-17 11:13:11,000] [INFO] Running command: cat /var/lib/cwl/stg6e92b2c6-5886-4818-be7c-baad9097c41e/OceanDNA-b22461.fa | prodigal -d OceanDNA-b22461/cds.fna -a OceanDNA-b22461/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:14:04,099] [INFO] Task succeeded: Prodigal
[2023-03-17 11:14:04,099] [INFO] Task started: HMMsearch
[2023-03-17 11:14:04,099] [INFO] Running command: hmmsearch --tblout OceanDNA-b22461/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdda84dea-06c1-4b2c-a0af-7a41255d3f56/dqc_reference/reference_markers.hmm OceanDNA-b22461/protein.faa > /dev/null
[2023-03-17 11:14:04,398] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:14:04,398] [INFO] Found 6/6 markers.
[2023-03-17 11:14:04,520] [INFO] Query marker FASTA was written to OceanDNA-b22461/markers.fasta
[2023-03-17 11:14:04,522] [INFO] Task started: Blastn
[2023-03-17 11:14:04,522] [INFO] Running command: blastn -query OceanDNA-b22461/markers.fasta -db /var/lib/cwl/stgdda84dea-06c1-4b2c-a0af-7a41255d3f56/dqc_reference/reference_markers.fasta -out OceanDNA-b22461/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:14:05,073] [INFO] Task succeeded: Blastn
[2023-03-17 11:14:05,104] [INFO] Selected 14 target genomes.
[2023-03-17 11:14:05,105] [INFO] Target genome list was writen to OceanDNA-b22461/target_genomes.txt
[2023-03-17 11:14:05,114] [INFO] Task started: fastANI
[2023-03-17 11:14:05,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e92b2c6-5886-4818-be7c-baad9097c41e/OceanDNA-b22461.fa --refList OceanDNA-b22461/target_genomes.txt --output OceanDNA-b22461/fastani_result.tsv --threads 1
[2023-03-17 11:14:24,831] [INFO] Task succeeded: fastANI
[2023-03-17 11:14:24,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdda84dea-06c1-4b2c-a0af-7a41255d3f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:14:24,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdda84dea-06c1-4b2c-a0af-7a41255d3f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:14:24,840] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 11:14:24,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 11:14:24,841] [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
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	96.1292	1983	2428	95	conclusive
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	88.8573	1979	2428	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	87.8559	1848	2428	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	83.7176	1618	2428	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	78.1635	326	2428	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	78.0188	209	2428	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.8813	305	2428	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	77.5774	327	2428	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	76.7119	227	2428	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:14:24,841] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22461/tc_result.tsv
[2023-03-17 11:14:24,841] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:14:24,841] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:14:24,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdda84dea-06c1-4b2c-a0af-7a41255d3f56/dqc_reference/checkm_data
[2023-03-17 11:14:24,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:14:24,852] [INFO] Task started: CheckM
[2023-03-17 11:14:24,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22461/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22461/checkm_input OceanDNA-b22461/checkm_result
[2023-03-17 11:17:00,337] [INFO] Task succeeded: CheckM
[2023-03-17 11:17:00,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:17:00,381] [INFO] ===== Completeness check finished =====
[2023-03-17 11:17:00,381] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:17:00,381] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22461/markers.fasta)
[2023-03-17 11:17:00,383] [INFO] Task started: Blastn
[2023-03-17 11:17:00,383] [INFO] Running command: blastn -query OceanDNA-b22461/markers.fasta -db /var/lib/cwl/stgdda84dea-06c1-4b2c-a0af-7a41255d3f56/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22461/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:17:01,148] [INFO] Task succeeded: Blastn
[2023-03-17 11:17:01,155] [INFO] Selected 11 target genomes.
[2023-03-17 11:17:01,156] [INFO] Target genome list was writen to OceanDNA-b22461/target_genomes_gtdb.txt
[2023-03-17 11:17:01,165] [INFO] Task started: fastANI
[2023-03-17 11:17:01,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e92b2c6-5886-4818-be7c-baad9097c41e/OceanDNA-b22461.fa --refList OceanDNA-b22461/target_genomes_gtdb.txt --output OceanDNA-b22461/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:17:18,556] [INFO] Task succeeded: fastANI
[2023-03-17 11:17:18,563] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:17:18,563] [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_000338295.1	s__Rhodopirellula europaea	96.1292	1983	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	conclusive
GCF_000196115.1	s__Rhodopirellula baltica	88.8364	1983	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	87.8634	1847	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027925.1	s__Rhodopirellula islandica	83.7326	1615	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	78.136	327	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752935.1	s__Crateriforma conspicua	78.0188	209	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_007859915.1	s__Rhodopirellula pilleata	77.5831	328	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192335.1	s__Rhodopirellula rubra	77.268	323	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_002901265.1	s__Stieleria baltica_A	76.7214	176	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_007860125.1	s__Rubripirellula tenax	76.7206	228	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	76.651	230	2428	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:17:18,576] [INFO] GTDB search result was written to OceanDNA-b22461/result_gtdb.tsv
[2023-03-17 11:17:18,597] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:17:18,611] [INFO] DFAST_QC result json was written to OceanDNA-b22461/dqc_result.json
[2023-03-17 11:17:18,612] [INFO] DFAST_QC completed!
[2023-03-17 11:17:18,612] [INFO] Total running time: 0h4m9s