[2023-03-16 10:35:17,657] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:35:17,657] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:35:17,658] [INFO] DQC Reference Directory: /var/lib/cwl/stgb42d7e05-4760-4951-a78c-d74dae81fa0e/dqc_reference
[2023-03-16 10:35:18,817] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:35:18,817] [INFO] Task started: Prodigal
[2023-03-16 10:35:18,818] [INFO] Running command: cat /var/lib/cwl/stg3f5aabc6-0a5a-46c4-8706-2739e7456378/OceanDNA-b22474.fa | prodigal -d OceanDNA-b22474/cds.fna -a OceanDNA-b22474/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:36:28,757] [INFO] Task succeeded: Prodigal
[2023-03-16 10:36:28,758] [INFO] Task started: HMMsearch
[2023-03-16 10:36:28,758] [INFO] Running command: hmmsearch --tblout OceanDNA-b22474/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb42d7e05-4760-4951-a78c-d74dae81fa0e/dqc_reference/reference_markers.hmm OceanDNA-b22474/protein.faa > /dev/null
[2023-03-16 10:36:29,315] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:36:29,315] [INFO] Found 6/6 markers.
[2023-03-16 10:36:29,421] [INFO] Query marker FASTA was written to OceanDNA-b22474/markers.fasta
[2023-03-16 10:36:29,426] [INFO] Task started: Blastn
[2023-03-16 10:36:29,427] [INFO] Running command: blastn -query OceanDNA-b22474/markers.fasta -db /var/lib/cwl/stgb42d7e05-4760-4951-a78c-d74dae81fa0e/dqc_reference/reference_markers.fasta -out OceanDNA-b22474/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:36:30,052] [INFO] Task succeeded: Blastn
[2023-03-16 10:36:30,053] [INFO] Selected 17 target genomes.
[2023-03-16 10:36:30,053] [INFO] Target genome list was writen to OceanDNA-b22474/target_genomes.txt
[2023-03-16 10:36:30,072] [INFO] Task started: fastANI
[2023-03-16 10:36:30,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f5aabc6-0a5a-46c4-8706-2739e7456378/OceanDNA-b22474.fa --refList OceanDNA-b22474/target_genomes.txt --output OceanDNA-b22474/fastani_result.tsv --threads 1
[2023-03-16 10:36:54,198] [INFO] Task succeeded: fastANI
[2023-03-16 10:36:54,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb42d7e05-4760-4951-a78c-d74dae81fa0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:36:54,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb42d7e05-4760-4951-a78c-d74dae81fa0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:36:54,207] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:36:54,207] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:36:54,207] [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 maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	84.2483	1731	2879	95	below_threshold
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	80.4198	1052	2879	95	below_threshold
Novipirellula artificiosorum	strain=Poly41	GCA_007860135.1	2528016	2528016	type	True	76.5261	304	2879	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	76.518	223	2879	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	76.513	260	2879	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	76.4577	257	2879	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	76.4214	203	2879	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	76.3711	220	2879	95	below_threshold
Novipirellula aureliae	strain=Q31b	GCA_007860185.1	2527966	2527966	type	True	76.344	247	2879	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.0962	205	2879	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	75.9842	212	2879	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	75.6718	169	2879	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:36:54,207] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22474/tc_result.tsv
[2023-03-16 10:36:54,208] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:36:54,208] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:36:54,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb42d7e05-4760-4951-a78c-d74dae81fa0e/dqc_reference/checkm_data
[2023-03-16 10:36:54,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:36:54,218] [INFO] Task started: CheckM
[2023-03-16 10:36:54,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22474/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22474/checkm_input OceanDNA-b22474/checkm_result
[2023-03-16 10:39:51,623] [INFO] Task succeeded: CheckM
[2023-03-16 10:39:51,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:39:51,632] [INFO] ===== Completeness check finished =====
[2023-03-16 10:39:51,632] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:39:51,632] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22474/markers.fasta)
[2023-03-16 10:39:51,634] [INFO] Task started: Blastn
[2023-03-16 10:39:51,634] [INFO] Running command: blastn -query OceanDNA-b22474/markers.fasta -db /var/lib/cwl/stgb42d7e05-4760-4951-a78c-d74dae81fa0e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22474/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:39:53,457] [INFO] Task succeeded: Blastn
[2023-03-16 10:39:53,458] [INFO] Selected 14 target genomes.
[2023-03-16 10:39:53,458] [INFO] Target genome list was writen to OceanDNA-b22474/target_genomes_gtdb.txt
[2023-03-16 10:39:53,507] [INFO] Task started: fastANI
[2023-03-16 10:39:53,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f5aabc6-0a5a-46c4-8706-2739e7456378/OceanDNA-b22474.fa --refList OceanDNA-b22474/target_genomes_gtdb.txt --output OceanDNA-b22474/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:40:20,726] [INFO] Task succeeded: fastANI
[2023-03-16 10:40:20,734] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:40:20,734] [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_000346295.1	s__Novipirellula maiorica	84.2529	1731	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860095.1	s__Novipirellula galeiformis	80.3803	1060	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007753675.1	s__Stieleria sp007753675	77.3158	303	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007859835.1	s__Novipirellula sp007859835	76.6937	306	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860125.1	s__Rubripirellula tenax	76.5358	258	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860135.1	s__Novipirellula artificiosorum	76.5262	305	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860175.1	s__Rubripirellula reticaptiva	76.4507	258	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860185.1	s__Novipirellula aureliae	76.3516	246	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901265.1	s__Stieleria baltica_A	76.1795	133	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_007860045.1	s__Stieleria varia	76.1037	204	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752935.1	s__Crateriforma conspicua	75.9837	212	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_014154935.1	s__Stieleria sp014154935	75.9358	248	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	75.6783	168	2879	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:40:20,734] [INFO] GTDB search result was written to OceanDNA-b22474/result_gtdb.tsv
[2023-03-16 10:40:20,734] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:40:20,736] [INFO] DFAST_QC result json was written to OceanDNA-b22474/dqc_result.json
[2023-03-16 10:40:20,736] [INFO] DFAST_QC completed!
[2023-03-16 10:40:20,736] [INFO] Total running time: 0h5m3s