Maybe the error arose because it is picking reference OTUs from the default greengenes fasta file, not the one I specified in my params file (see line 38 of log file).
pick_otus.py -i filtered_R1.fasta -o open_reference_otus4//step1_otus_test -r /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta -m usearch61_ref --enable_rev_strand_match --suppress_new_clusters
abundance_sorted.uc:
(head)
S 0 204 * * * * * BY.1.1.6_3 *
H 0 204 100.0 * 0 0 * BY.1.1.6_4 BY.1.1.6_3
H 0 204 100.0 * 0 0 * BY.1.1.6_5 BY.1.1.6_3
H 0 204 100.0 * 0 0 * BY.1.1.6_6 BY.1.1.6_3
H 0 204 100.0 * 0 0 * BY.1.1.6_7 BY.1.1.6_3
H 0 204 100.0 * 0 0 * BY.1.1.6_8 BY.1.1.6_3
H 0 204 100.0 * 0 0 * BY.1.1.6_9 BY.1.1.6_3
H 0 204 100.0 * 0 0 * BY.1.1.6_10 BY.1.1.6_3
H 0 204 100.0 * 0 0 * BY.1.1.6_11 BY.1.1.6_3
H 0 204 100.0 * 0 0 * BY.1.1.6_12 BY.1.1.6_3
(tail)
C 341555 1 * * * * * BY.14.4.6_848000 *
C 341556 1 * * * * * BY.14.4.6_847989 *
C 341557 1 * * * * * BY.1.4.6_62403 *
C 341558 1 * * * * * BY.14.4.6_847986 *
C 341559 1 * * * * * BY.14.4.6_847987 *
C 341560 1 * * * * * BY.14.4.6_847992 *
C 341561 1 * * * * * BY.14.4.6_847996 *
C 341562 1 * * * * * BY.14.4.6_847997 *
C 341563 1 * * * * * BY.14.4.6_847993 *
C 341564 1 * * * * * BY.14.4.6_847994 *
ref_clustered.uc:
empty
the error:
File "/home/obrett/my_env/lib/python2.7/site-packages/bfillings/usearch.py", line 1844, in usearch61_ref_cluster
raise ApplicationError('Error running usearch61. Possible causes are '
burrito.util.ApplicationError: Error running usearch61. Possible causes are unsupported version (current supported version is usearch v6.1.544) is installed or improperly formatted input file was provided
-Brett
pick_otus.py -i filtered_R1.fasta -o open_reference_otus4//step1_otus_test2 -r /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta -m uclust_ref --enable_rev_strand_match --suppress_new_clusters
Filtered_R1_clusters.uc:
# uclust --input /tmp/UclustExactMatchFilteryq6urR.fasta --id 0.97 --tmpdir /tmp --rev --w 8 --stepwords 8 --usersort --maxaccepts 1 --libonly --stable_sort --maxrejects 8 --lib /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta --uc open_reference_otus4//step1_otus_test2/filtered_R1_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
The error:
File "/home/obrett/my_env/lib/python2.7/site-packages/bfillings/uclust.py", line 585, in get_clusters_from_fasta_filepath
raise ApplicationError('Error running uclust. Possible causes are '
burrito.util.ApplicationError: Error running uclust. Possible causes are unsupported version (current supported version is v1.2.22) is installed or improperly formatted input file was provided
Thanks,
Brett
# uclust --input /tmp/UclustExactMatchFilterxE2Xs4.fasta --id 0.97 --tmpdir /tmp --rev --w 8 --stepwords 8 --usersort --maxaccepts 1 --libonly --stable_sort --maxrejects 8 --lib /workspace/scratch/obrett/processing/subset_reads.fna --uc test_subset_otu_picking/filtered_R1_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
L 2 204 * * * * * BY.1.1.6_3 *
H 2 204 100.0 + 0 0 204M QiimeExactMatch.BY.1.1.6_3 BY.1.1.6_3
(tail)
D 1 7941 * * * * 97.8 BY.1.1.6_2 *
D 2 76530 * * * * 98.3 BY.1.1.6_3 *
D 17 15 * * * * 97.8 BY.1.1.6_18 *
D 18 13 * * * * 98.6 BY.1.1.6_19 *
D 24 115 * * * * 97.5 BY.1.1.6_25 *
D 29 5 * * * * 97.5 BY.1.1.6_30 *
D 34 109 * * * * 98.5 BY.1.1.6_35 *
D 37 70 * * * * 98.3 BY.1.1.6_38 *
D 42 158 * * * * 98.1 BY.1.1.6_43 *
D 47 312 * * * * 98.1 BY.1.1.6_48 *
The directory also contains a log, failures, and the otu map. Let me know if you'd like to see any of them. Think I should download a new reference fasta file?
Thanks,
Brett
pick_otus.py -i filtered_R1.fasta -o open_reference_otus5 -r /home/obrett/UNITE2/parsed_97.fasta -m uclust_ref --enable_rev_strand_match --suppress_new_clusters
filtered_R1_clusters.uc:
(head)
# uclust --input /tmp/UclustExactMatchFilter8VaWtf.fasta --id 0.97 --tmpdir /tmp --rev --w 8 --stepwords 8 --usersort --maxaccepts 1 --libonly --stable_sort --maxrejects 8 --lib /home/obrett/UNITE2/parsed_97.fasta --uc open_reference_otus5/filtered_R1_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
N * 204 * * * * * QiimeExactMatch.BY.1.1.6_3 *
N * 204 * * * * * QiimeExactMatch.BY.1.1.6_68 *
(tail)
D 7849 307 * * * * 97.7 SH032625.07FU_KF757018_reps_singleton *
D 13146 58 * * * * 97.4 SH032623.07FU_KF757009_reps_singleton *
D 13899 7 * * * * 97.2 SH011608.07FU_KF150318_reps *
D 14048 2 * * * * 98.8 SH005938.07FU_EF530941_reps *
D 14393 3 * * * * 97.6 SH001842.07FU_UDB015619_refs *
D 15515 2 * * * * 97.9 SH467507.07FU_FJ152489_reps_singleton *
D 17888 44 * * * * 97.5 SH028821.07FU_EF679363_refs *
D 25193 2 * * * * 97.4 SH014640.07FU_UDB017896_refs *
D 29378 3 * * * * 97.2 SH018304.07FU_UDB015265_refs *
D 36805 3 * * * * 97.3 SH012620.07FU_UDB011614_refs *
log file attached
-Brett
formatdb -l "parsed_97_dynamic.fasta.log" -o T -n "parsed_97_dynamic.fasta" -i "/home/obrett/UNITE2/parsed_97_dynamic.fasta" -p F
directly?
-bash: /home/obrett/blast-2.2.22/bin/formatdb: cannot execute binary file