search

sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
268 stars 67 forks source link

[main_cat] ERROR: input is not BAM or CRAM #385

Closed Thomas0194 closed 6 months ago

Thomas0194 commented 6 months ago

Hi,

I'm having issues while starting zUMIs as follows,

This problem confused me for a while,

I ran the file in Ubuntu and also tried changing all the paths from /mnt/d to the wsl file folder.

However, the error still appears.

Do you know what's wrong with it and could you please give me some suggestions?

Thanks a lot

Best,

zUMIs.txt

Using miniconda environment for zUMIs! note: internal executables will be used instead of those specified in the YAML file!

You provided these parameters: YAML file: zUMIs.yaml zUMIs directory: /mnt/d/zUMIs-main STAR executable STAR samtools executable samtools pigz executable pigz Rscript executable Rscript RAM limit: null zUMIs version 2.9.7e

Mon Jan 8 17:41:35 JST 2024 WARNING: The STAR version used for mapping is 2.7.11a and the STAR index was created using the version 2.7.4a. This may lead to an error while mapping. If you encounter any errors at the mapping stage, please make sure to create the STAR index using STAR 2.7.11a. Filtering... Mon Jan 8 17:42:46 JST 2024 [1] "180 barcodes detected." [1] "961431 reads were assigned to barcodes that do not correspond to intact cells." [1] "Found 386 daughter barcodes that can be binned into 148 parent barcodes." [1] "Binned barcodes correspond to 78143 reads." Mapping... [1] "2024-01-08 17:43:00 JST" STAR --readFilesCommand samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --genomeDir /mnt/d/P3_Far_S1_CMLC-zumi_test_file/STAR_Reference/STAR_index --sjdbGTFfile /mnt/d/P3_Far_S1_CMLC-zumi_test_file/STAR_Reference/Homo_sapiens.GRCh38.110.gtf --runThreadN 3 --sjdbOverhang 65 --readFilesType SAM SE --twopassMode Basic --readFilesIn /home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121ai.filtered.tagged.bam,/home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121aj.filtered.tagged.bam,/home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121ak.filtered.tagged.bam --outFileNamePrefix /home/thomaslio/test/zUMIs_output/.tmpMap//tmp.Project121.3. STAR version: 2.7.11a compiled: 2023-08-15T11:38:34-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jan 08 17:43:05 ..... started STAR run Jan 08 17:43:06 ..... loading genome STAR --readFilesCommand samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --genomeDir /mnt/d/P3_Far_S1_CMLC-zumi_test_file/STAR_Reference/STAR_index --sjdbGTFfile /mnt/d/P3_Far_S1_CMLC-zumi_test_file/STAR_Reference/Homo_sapiens.GRCh38.110.gtf --runThreadN 3 --sjdbOverhang 65 --readFilesType SAM SE --twopassMode Basic --readFilesIn /home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121aa.filtered.tagged.bam,/home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121ab.filtered.tagged.bam,/home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121ac.filtered.tagged.bam,/home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121ad.filtered.tagged.bam --outFileNamePrefix /home/thomaslio/test/zUMIs_output/.tmpMap//tmp.Project121.1. STAR version: 2.7.11a compiled: 2023-08-15T11:38:34-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jan 08 17:43:05 ..... started STAR run Jan 08 17:43:06 ..... loading genome STAR --readFilesCommand samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --genomeDir /mnt/d/P3_Far_S1_CMLC-zumi_test_file/STAR_Reference/STAR_index --sjdbGTFfile /mnt/d/P3_Far_S1_CMLC-zumi_test_file/STAR_Reference/Homo_sapiens.GRCh38.110.gtf --runThreadN 3 --sjdbOverhang 65 --readFilesType SAM SE --twopassMode Basic --readFilesIn /home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121ae.filtered.tagged.bam,/home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121af.filtered.tagged.bam,/home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121ag.filtered.tagged.bam,/home/thomaslio/test/zUMIs_output/.tmpMerge//Project121.Project121ah.filtered.tagged.bam --outFileNamePrefix /home/thomaslio/test/zUMIs_output/.tmpMap//tmp.Project121.2. STAR version: 2.7.11a compiled: 2023-08-15T11:38:34-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jan 08 17:43:05 ..... started STAR run Jan 08 17:43:06 ..... loading genome Jan 08 17:44:16 ..... processing annotations GTF Jan 08 17:46:05 ..... inserting junctions into the genome indices Jan 08 17:47:19 ..... started 1st pass mapping Jan 08 17:47:46 ..... finished 1st pass mapping Jan 08 17:47:46 ..... inserting junctions into the genome indices Jan 08 17:48:41 ..... started mapping Jan 08 17:49:19 ..... finished mapping Jan 08 17:49:19 ..... finished successfully [main_cat] ERROR: input is not BAM or CRAM [main_cat] ERROR: input is not BAM or CRAM Mon Jan 8 17:49:21 JST 2024 Counting... [1] "2024-01-08 17:49:41 JST" [1] "4.5e+08 Reads per chunk" [1] "Loading reference annotation from:" [1] "/home/thomaslio/test/Project121.final_annot.gtf" [E::hts_open_format] Failed to open file /home/thomaslio/test/Project121.filtered.tagged.Aligned.out.bam samtools view: failed to open "/home/thomaslio/test/Project121.filtered.tagged.Aligned.out.bam" for reading: No such file or directory [E::hts_open_format] Failed to open file /home/thomaslio/test/Project121.filtered.tagged.Aligned.out.bam samtools view: failed to open "/home/thomaslio/test/Project121.filtered.tagged.Aligned.out.bam" for reading: No such file or directory Error in gsub("SN:", "", chr) : object 'chr' not found Calls: .makeSAF ... .chromLengthFilter -> [ -> [.data.table -> eval -> eval -> gsub In addition: Warning message: In data.table::fread(bread, col.names = c("chr", "len"), header = F) : File '/tmp/Rtmp32axoi/file7e5b964e69974' has size 0. Returning a NULL data.table. Execution halted Mon Jan 8 17:49:51 JST 2024 Loading required package: yaml Loading required package: Matrix [1] "loomR found" Error in gzfile(file, "rb") : cannot open the connection Calls: rds_to_loom -> readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/home/thomaslio/test/zUMIs_output/expression/Project121.dgecounts.rds', probable reason 'No such file or directory' Execution halted Mon Jan 8 17:49:59 JST 2024 Descriptive statistics... [1] "I am loading useful packages for plotting..." [1] "2024-01-08 17:50:01 JST" Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/home/thomaslio/test/zUMIs_output/expression/Project121.dgecounts.rds', probable reason 'No such file or directory' Execution halted Mon Jan 8 17:50:11 JST 2024

cziegenhain commented 6 months ago

Hi,

Seems like there is a problem loading the STAR index during mapping. I recommend to repeat the genome generation step and try again! All the best, Christoph

8 jan. 2024 kl. 07:47 skrev Thomas0194 @.***>:

Hi,

I'm having issues while starting zUMIs as follows,

This problem confused me for a while,

I ran the file in Ubuntu and also tried changing all the paths from /mnt/d to the wsl file folder.

However, the error still appears.

Do you know what's wrong with it and could you please give me some suggestions?

Thanks a lot

Best,

zUMIs.txt https://github.com/sdparekh/zUMIs/files/13856899/zUMIs.txt Using miniconda environment for zUMIs! note: internal executables will be used instead of those specified in the YAML file!

You provided these parameters: YAML file: zUMIs.yaml zUMIs directory: /mnt/d/zUMIs-main STAR executable STAR samtools executable samtools pigz executable pigz Rscript executable Rscript RAM limit: null zUMIs version 2.9.7e

Mon Jan 8 15:25:45 JST 2024 Filtering... Mon Jan 8 15:27:03 JST 2024 [1] "180 barcodes detected." [1] "961431 reads were assigned to barcodes that do not correspond to intact cells." [1] "Found 386 daughter barcodes that can be binned into 148 parent barcodes." [1] "Binned barcodes correspond to 78143 reads." Mapping... [1] "2024-01-08 15:27:19 JST" Jan 08 15:27:25 ..... started STAR run Jan 08 15:27:25 ..... started STAR run Jan 08 15:27:26 ..... loading genome Jan 08 15:27:26 ..... loading genome

EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt" SOLUTION: use correct parameter name (check the manual)

Jan 08 15:27:26 ...... FATAL ERROR, exiting Jan 08 15:27:25 ..... started STAR run

EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt" SOLUTION: use correct parameter name (check the manual)

Jan 08 15:27:26 ...... FATAL ERROR, exiting Jan 08 15:27:26 ..... loading genome

EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt" SOLUTION: use correct parameter name (check the manual)

Jan 08 15:27:26 ...... FATAL ERROR, exiting cp: cannot stat '/home/thomaslio/test/zUMIs_output/.tmpMap//tmp.test_file.*.SJ.out.tab': No such file or directory [main_cat] ERROR: input is not BAM or CRAM [main_cat] ERROR: input is not BAM or CRAM Mon Jan 8 15:27:26 JST 2024 Counting... [1] "2024-01-08 15:27:44 JST" [1] "4.5e+08 Reads per chunk" [1] "Loading reference annotation from:" [1] "/home/thomaslio/test/test_file.final_annot.gtf" [E::hts_open_format] Failed to open file /home/thomaslio/test/test_file.filtered.tagged.Aligned.out.bam samtools view: failed to open "/home/thomaslio/test/test_file.filtered.tagged.Aligned.out.bam" for reading: No such file or directory [E::hts_open_format] Failed to open file /home/thomaslio/test/test_file.filtered.tagged.Aligned.out.bam samtools view: failed to open "/home/thomaslio/test/test_file.filtered.tagged.Aligned.out.bam" for reading: No such file or directory Error in gsub("SN:", "", chr) : object 'chr' not found Calls: .makeSAF ... .chromLengthFilter -> [ -> [.data.table -> eval -> eval -> gsub In addition: Warning message: In data.table::fread(bread, col.names = c("chr", "len"), header = F) : File '/tmp/Rtmp9QW8F5/file2a4e0763c691a' has size 0. Returning a NULL data.table. Execution halted Mon Jan 8 15:27:53 JST 2024 Loading required package: yaml Loading required package: Matrix [1] "loomR found" Error in gzfile(file, "rb") : cannot open the connection Calls: rds_to_loom -> readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/home/thomaslio/test/zUMIs_output/expression/test_file.dgecounts.rds', probable reason 'No such file or directory' Execution halted Mon Jan 8 15:27:59 JST 2024 Descriptive statistics... [1] "I am loading useful packages for plotting..." [1] "2024-01-08 15:28:01 JST" Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/home/thomaslio/test/zUMIs_output/expression/test_file.dgecounts.rds', probable reason 'No such file or directory' Execution halted Mon Jan 8 15:28:11 JST 2024

— Reply to this email directly, view it on GitHub https://github.com/sdparekh/zUMIs/issues/385, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD6PWY3L2NFJGKKOBGEQREDYNOJBFAVCNFSM6AAAAABBQ7A3BCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DSOBSGAZTGMA. You are receiving this because you are subscribed to this thread.

Thomas0194 commented 6 months ago

Hi Christoph,

Thanks for your suggestion,

I fixed the problem after receiving your useful suggestion!

Thanks a lot!

Best,