[2023-03-15 23:07:02,632] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,632] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,632] [INFO] DQC Reference Directory: /var/lib/cwl/stga2d42746-ec25-4d4d-a219-2a9db56e8536/dqc_reference
[2023-03-15 23:07:03,965] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,966] [INFO] Running command: cat /var/lib/cwl/stg567dc33d-6e57-4795-9bcd-ba5fe40a8281/OceanDNA-b47086.fa | prodigal -d OceanDNA-b47086/cds.fna -a OceanDNA-b47086/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:08:01,853] [INFO] Task succeeded: Prodigal
[2023-03-15 23:08:01,854] [INFO] Task started: HMMsearch
[2023-03-15 23:08:01,854] [INFO] Running command: hmmsearch --tblout OceanDNA-b47086/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2d42746-ec25-4d4d-a219-2a9db56e8536/dqc_reference/reference_markers.hmm OceanDNA-b47086/protein.faa > /dev/null
[2023-03-15 23:08:02,107] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:08:02,108] [INFO] Found 6/6 markers.
[2023-03-15 23:08:02,154] [INFO] Query marker FASTA was written to OceanDNA-b47086/markers.fasta
[2023-03-15 23:08:02,155] [INFO] Task started: Blastn
[2023-03-15 23:08:02,155] [INFO] Running command: blastn -query OceanDNA-b47086/markers.fasta -db /var/lib/cwl/stga2d42746-ec25-4d4d-a219-2a9db56e8536/dqc_reference/reference_markers.fasta -out OceanDNA-b47086/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:08:02,693] [INFO] Task succeeded: Blastn
[2023-03-15 23:08:02,704] [INFO] Selected 23 target genomes.
[2023-03-15 23:08:02,704] [INFO] Target genome list was writen to OceanDNA-b47086/target_genomes.txt
[2023-03-15 23:08:02,792] [INFO] Task started: fastANI
[2023-03-15 23:08:02,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg567dc33d-6e57-4795-9bcd-ba5fe40a8281/OceanDNA-b47086.fa --refList OceanDNA-b47086/target_genomes.txt --output OceanDNA-b47086/fastani_result.tsv --threads 1
[2023-03-15 23:08:20,774] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:20,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2d42746-ec25-4d4d-a219-2a9db56e8536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:08:20,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2d42746-ec25-4d4d-a219-2a9db56e8536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:08:20,782] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:08:20,782] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:08:20,782] [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
Prosthecobacter debontii	strain=ATCC 700200	GCA_900167535.1	48467	48467	type	True	76.8443	126	1954	95	below_threshold
Prosthecobacter fusiformis	strain=ATCC 25309	GCA_004364345.1	48464	48464	type	True	76.6562	119	1954	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	76.602	229	1954	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	76.4054	205	1954	95	below_threshold
Prosthecobacter dejongeii	strain=DSM 12251	GCA_014203045.1	48465	48465	type	True	76.2443	144	1954	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	76.1411	126	1954	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	76.0937	110	1954	95	below_threshold
Verrucomicrobium spinosum	strain=JCM 18804	GCA_001313125.1	2736	2736	type	True	75.9793	111	1954	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	75.6169	59	1954	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:08:20,782] [INFO] DFAST Taxonomy check result was written to OceanDNA-b47086/tc_result.tsv
[2023-03-15 23:08:20,782] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:08:20,782] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:08:20,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2d42746-ec25-4d4d-a219-2a9db56e8536/dqc_reference/checkm_data
[2023-03-15 23:08:20,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:08:20,805] [INFO] Task started: CheckM
[2023-03-15 23:08:20,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b47086/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b47086/checkm_input OceanDNA-b47086/checkm_result
[2023-03-15 23:10:56,442] [INFO] Task succeeded: CheckM
[2023-03-15 23:10:56,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:10:56,447] [INFO] ===== Completeness check finished =====
[2023-03-15 23:10:56,447] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:10:56,447] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b47086/markers.fasta)
[2023-03-15 23:10:56,448] [INFO] Task started: Blastn
[2023-03-15 23:10:56,448] [INFO] Running command: blastn -query OceanDNA-b47086/markers.fasta -db /var/lib/cwl/stga2d42746-ec25-4d4d-a219-2a9db56e8536/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b47086/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:10:57,198] [INFO] Task succeeded: Blastn
[2023-03-15 23:10:57,199] [INFO] Selected 21 target genomes.
[2023-03-15 23:10:57,199] [INFO] Target genome list was writen to OceanDNA-b47086/target_genomes_gtdb.txt
[2023-03-15 23:10:57,569] [INFO] Task started: fastANI
[2023-03-15 23:10:57,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg567dc33d-6e57-4795-9bcd-ba5fe40a8281/OceanDNA-b47086.fa --refList OceanDNA-b47086/target_genomes_gtdb.txt --output OceanDNA-b47086/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:11:19,823] [INFO] Task succeeded: fastANI
[2023-03-15 23:11:19,835] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:11:19,835] [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_017301975.1	s__Prosthecobacter sp017301975	77.7081	254	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506995.1	s__Prosthecobacter sp003506995	77.2567	238	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279765.1	s__Prosthecobacter sp002279765	76.9207	225	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167535.1	s__Prosthecobacter debontii	76.8851	124	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838675.1	s__Prosthecobacter sp903838675	76.845	201	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.92	99.91	0.96	0.96	3	-
GCA_019186985.1	s__Prosthecobacter sp019186985	76.8359	222	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848465.1	s__Prosthecobacter sp903848465	76.824	193	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.97	99.92	0.97	0.96	6	-
GCA_002482965.1	s__Prosthecobacter sp002482965	76.7972	227	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343505.1	s__Prosthecobacter sp002343505	76.793	234	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	98.23	97.36	0.90	0.88	4	-
GCA_017853885.1	s__Prosthecobacter sp017853885	76.7305	109	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795375.1	s__Prosthecobacter sp016795375	76.7119	202	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713035.1	s__Prosthecobacter sp016713035	76.7095	179	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364345.1	s__Prosthecobacter fusiformis	76.6562	119	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203095.1	s__Prosthecobacter vanneervenii	76.6228	225	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960845.1	s__Prosthecobacter sp903960845	76.5752	179	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.18	98.90	0.84	0.82	4	-
GCA_002336895.1	s__Prosthecobacter sp002336895	76.5622	240	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011044495.1	s__Roseimicrobium sp011044495	76.1658	114	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Roseimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172155.1	s__Verrucomicrobium spinosum	76.1236	108	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	99.88	99.88	1.00	1.00	2	-
GCA_000739635.1	s__Verrucomicrobium sp000739635	76.0892	122	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005780165.1	s__Phragmitibacter flavus	76.0881	97	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Phragmitibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739655.1	s__Verrucomicrobium sp000739655	76.0188	131	1954	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:11:19,835] [INFO] GTDB search result was written to OceanDNA-b47086/result_gtdb.tsv
[2023-03-15 23:11:19,835] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:11:19,837] [INFO] DFAST_QC result json was written to OceanDNA-b47086/dqc_result.json
[2023-03-15 23:11:19,837] [INFO] DFAST_QC completed!
[2023-03-15 23:11:19,837] [INFO] Total running time: 0h4m17s