### q2-2019.10 ERROR:root:could not perform read merging with BBmerge. Error from BBmerge was: java -Djava.library.path=/opt/miniconda3/envs/qiime2-2019.10/opt/bbmap-38.18/jni/ -ea -Xmx1000m -Xms1000m -cp /opt/miniconda3/envs/qiime2-2019.10/opt/bbmap-38.18/current/ jgi.BBMerge in=/tmp/qiime2-archive-0mpexh0q/337ee93b-a314-4bb4-88e6-7f643d28e47d/data/ITS1-SFB-MP-000799_0_L001_R1_001.fastq.gz out=/tmp/itsxpress_pyhvhg3r/seq.fq.gz t=12 maxmismatches=40 maxratio=0.3 Executing jgi.BBMerge [in=/tmp/qiime2-archive-0mpexh0q/337ee93b-a314-4bb4-88e6-7f643d28e47d/data/ITS1-SFB-MP-000799_0_L001_R1_001.fastq.gz, out=/tmp/itsxpress_pyhvhg3r/seq.fq.gz, t=12, maxmismatches=40, maxratio=0.3] Version 38.18 Set threads to 12 Exception in thread "main" java.lang.RuntimeException: Unknown parameter maxmismatches=40 at jgi.BBMerge.(BBMerge.java:644) at jgi.BBMerge.main(BBMerge.java:49) Traceback (most recent call last): File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/itsxpress/main.py", line 616, in _merge_reads p1.check_returncode() File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 369, in check_returncode self.stderr) subprocess.CalledProcessError: Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-0mpexh0q/337ee93b-a314-4bb4-88e6-7f643d28e47d/data/ITS1-SFB-MP-000799_0_L001_R1_001.fastq.gz', 'out=/tmp/itsxpress_pyhvhg3r/seq.fq.gz', 't=12', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1. Traceback (most recent call last): File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in __call__ results = action(**arguments) File "", line 2, in trim_single File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable output_types, provenance) File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_ output_views = self._callable(**view_args) File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py", line 123, in trim_single cluster_id=cluster_id) File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py", line 203, in main threads=threads) File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py", line 75, in _set_fastqs_and_check sobj._merge_reads(threads=threads) File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/itsxpress/main.py", line 620, in _merge_reads raise e File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/itsxpress/main.py", line 616, in _merge_reads p1.check_returncode() File "/opt/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 369, in check_returncode self.stderr) subprocess.CalledProcessError: Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-0mpexh0q/337ee93b-a314-4bb4-88e6-7f643d28e47d/data/ITS1-SFB-MP-000799_0_L001_R1_001.fastq.gz', 'out=/tmp/itsxpress_pyhvhg3r/seq.fq.gz', 't=12', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1. ### q2-2021.2 ERROR:root:could not perform read merging with BBmerge. Error from BBmerge was: java -Djava.library.path=/opt/miniconda3/envs/qiime2-2021.2/opt/bbmap-38.18/jni/ -ea -Xmx1000m -Xms1000m -cp /opt/miniconda3/envs/qiime2-2021.2/opt/bbmap-38.18/current/ jgi.BBMerge in=/tmp/qiime2-archive-ff61e34x/337ee93b-a314-4bb4-88e6-7f643d28e47d/data/ITS1-SFB-MP-000799_0_L001_R1_001.fastq.gz out=/tmp/itsxpress_bpqjstp7/seq.fq.gz t=12 maxmismatches=40 maxratio=0.3 Executing jgi.BBMerge [in=/tmp/qiime2-archive-ff61e34x/337ee93b-a314-4bb4-88e6-7f643d28e47d/data/ITS1-SFB-MP-000799_0_L001_R1_001.fastq.gz, out=/tmp/itsxpress_bpqjstp7/seq.fq.gz, t=12, maxmismatches=40, maxratio=0.3] Version 38.18 Set threads to 12 Exception in thread "main" java.lang.RuntimeException: Unknown parameter maxmismatches=40 at jgi.BBMerge.(BBMerge.java:644) at jgi.BBMerge.main(BBMerge.java:49) Traceback (most recent call last): File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/itsxpress/main.py", line 616, in _merge_reads p1.check_returncode() File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/subprocess.py", line 389, in check_returncode self.stderr) subprocess.CalledProcessError: Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-ff61e34x/337ee93b-a314-4bb4-88e6-7f643d28e47d/data/ITS1-SFB-MP-000799_0_L001_R1_001.fastq.gz', 'out=/tmp/itsxpress_bpqjstp7/seq.fq.gz', 't=12', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1. Traceback (most recent call last): File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__ results = action(**arguments) File "", line 2, in trim_single File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable output_types, provenance) File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callable_executor_ output_views = self._callable(**view_args) File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py", line 123, in trim_single cluster_id=cluster_id) File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py", line 203, in main threads=threads) File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py", line 75, in _set_fastqs_and_check sobj._merge_reads(threads=threads) File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/itsxpress/main.py", line 620, in _merge_reads raise e File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/itsxpress/main.py", line 616, in _merge_reads p1.check_returncode() File "/opt/miniconda3/envs/qiime2-2021.2/lib/python3.6/subprocess.py", line 389, in check_returncode self.stderr) subprocess.CalledProcessError: Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-ff61e34x/337ee93b-a314-4bb4-88e6-7f643d28e47d/data/ITS1-SFB-MP-000799_0_L001_R1_001.fastq.gz', 'out=/tmp/itsxpress_bpqjstp7/seq.fq.gz', 't=12', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1. vsearch v2.7.0_linux_x86_64, 125.6GB RAM, 12 cores https://github.com/torognes/vsearch ### q2-2021.11 Fatal error: File too small ERROR:root:Could not perform clustering with Vsearch. Error from Vsearch was: vsearch v2.7.0_linux_x86_64, 125.6GB RAM, 12 cores https://github.com/torognes/vsearch Fatal error: File too small Traceback (most recent call last): File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/itsxpress/main.py", line 540, in cluster p2.check_returncode() File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/subprocess.py", line 448, in check_returncode raise CalledProcessError(self.returncode, self.args, self.stdout, subprocess.CalledProcessError: Command '['vsearch', '--cluster_size', '/tmp/itsxpress_1fh_2082/seq.fq.gz', '--centroids', '/tmp/itsxpress_1fh_2082/rep.fa', '--uc', '/tmp/itsxpress_1fh_2082/uc.txt', '--strand', 'both', '--id', '0.995', '--threads', '12']' returned non-zero exit status 1. Traceback (most recent call last): File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__ results = action(**arguments) File "", line 2, in trim_single File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable outputs = self._callable_executor_(scope, callable_args, File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in _callable_executor_ output_views = self._callable(**view_args) File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_itsxpress/_itsxpress.py", line 116, in trim_single results = main(per_sample_sequences=per_sample_sequences, File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_itsxpress/_itsxpress.py", line 208, in main sobj.cluster(threads=threads, cluster_id=cluster_id) File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/itsxpress/main.py", line 543, in cluster raise e File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/itsxpress/main.py", line 540, in cluster p2.check_returncode() File "/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/subprocess.py", line 448, in check_returncode raise CalledProcessError(self.returncode, self.args, self.stdout, subprocess.CalledProcessError: Command '['vsearch', '--cluster_size', '/tmp/itsxpress_1fh_2082/seq.fq.gz', '--centroids', '/tmp/itsxpress_1fh_2082/rep.fa', '--uc', '/tmp/itsxpress_1fh_2082/uc.txt', '--strand', 'both', '--id', '0.995', '--threads', '12']' returned non-zero exit status 1. vsearch v2.7.0_linux_x86_64, 125.6GB RAM, 12 cores https://github.com/torognes/vsearch