slurmstepd: error: couldn't chdir to `/srv/pulsar/main/venv/lib/python3.6/site-packages': No such file or directory: going to /tmp instead

[2020-09-14 19:52:52] Beginning TopHat run (v2.1.1)
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[2020-09-14 19:52:52] Checking for Bowtie
		  Bowtie version:	 2.2.8.0
[2020-09-14 19:52:53] Checking for Bowtie index files (genome)..
[2020-09-14 19:52:55] Checking for reference FASTA file
[2020-09-14 19:52:55] Generating SAM header for /cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full
[2020-09-14 19:53:58] Preparing reads
	 left reads: min. length=76, max. length=76, 156798 kept reads (0 discarded)
[2020-09-14 19:54:12] Mapping left_kept_reads to genome hg19full with Bowtie2 
[2020-09-14 19:54:40] Mapping left_kept_reads_seg1 to genome hg19full with Bowtie2 (1/3)
[2020-09-14 19:54:50] Mapping left_kept_reads_seg2 to genome hg19full with Bowtie2 (2/3)
[2020-09-14 19:54:57] Mapping left_kept_reads_seg3 to genome hg19full with Bowtie2 (3/3)
[2020-09-14 19:55:04] Searching for junctions via segment mapping
[2020-09-14 19:57:35] Retrieving sequences for splices
[2020-09-14 19:58:55] Indexing splices
Building a SMALL index
[2020-09-14 19:59:03] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-09-14 19:59:06] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-09-14 19:59:10] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-09-14 19:59:14] Joining segment hits
[2020-09-14 20:00:42] Reporting output tracks
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[2020-09-14 20:02:35] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt
[2020-09-14 20:02:35] Run complete: 00:09:43 elapsed
[E::idx_find_and_load] Could not retrieve index file for '/jetstream/scratch0/main/jobs/30603555/working/tophat_out/accepted_hits.bam'
[E::idx_find_and_load] Could not retrieve index file for '/jetstream/scratch0/main/jobs/30603555/working/tophat_out/accepted_hits.bam'