Error messages from nextflow run main_AmrPlusPlus_v2_withRGI.nf

[srjun]

Hello,

I have error messages with the following command on the dataset provided. Could you let me know if these errors can be ignored? Thank you.

nextflow run main_AmrPlusPlus_v2_withRGI.nf -profile singularity --card_db card.json --output test_results_rgi --work work_rgi

N E X T F L O W ~ version 20.10.0 Launching main_AmrPlusPlus_v2_withRGI.nf [confident_williams] - revision: 77e0805d3d executor > local (24) executor > local (24) executor > local (24) executor > local (26) executor > local (29) executor > local (29) executor > local (33) executor > local (33) executor > local (38) executor > local (38) executor > local (40) executor > local (42) executor > local (42) executor > local (50) [54/f091c8] process > RunQC (S3_test) [100%] 3 of 3 ✔ [07/ce9c30] process > QCStats (null) [100%] 1 of 1 ✔ [91/995fb9] process > BuildHostIndex (chr21.fasta) [100%] 1 of 1 ✔ [09/955719] process > AlignReadsToHost (S3_test) [100%] 3 of 3 ✔ [07/bf7774] process > RemoveHostDNA (S3_test) [100%] 3 of 3 ✔ [c3/d3d4c0] process > HostRemovalStats (null) [100%] 1 of 1 ✔ [91/7a3a57] process > NonHostReads (S3_test) [100%] 3 of 3 ✔ [6c/da3027] process > BuildAMRIndex (megares_full_database_v2.00) [100%] 1 of 1 ✔ [d2/c7903b] process > AlignToAMR (S3_test) [100%] 3 of 3 ✔ [a3/5eaa14] process > RunResistome (S3_test) [100%] 3 of 3 ✔ [c7/ae4919] process > ResistomeResults (null) [100%] 1 of 1 ✔ [24/8e506c] process > SamDedupRunResistome (S3_test) [100%] 3 of 3 ✔ [9d/570580] process > SamDedupResistomeResults (null) [100%] 1 of 1 ✔ [79/3f6a11] process > RunRarefaction (S3_test) [100%] 3 of 3 ✔ [c1/2a5057] process > ExtractSNP (S3_test) [100%] 3 of 3 ✔ [07/0a6bbe] process > RunRGI (S3_test) [100%] 3 of 3 ✔ [fd/ca80a7] process > SNPconfirmation (S3_test) [100%] 3 of 3, failed: 3 ✔ [- ] process > Confirmed_AMR_hits - [9e/211eb5] process > Confirmed_ResistomeResults (null) [100%] 1 of 1, failed: 1 ✔ [bb/57da0f] process > ExtractDedupSNP (S3_test) [100%] 3 of 3 ✔ [ac/2f99a4] process > RunDedupRGI (S3_test) [100%] 3 of 3 ✔ [1e/8779a5] process > DedupSNPconfirmation (S3_test) [100%] 3 of 3, failed: 3 ✔ [- ] process > ConfirmDedupAMRHits - [f8/27c008] process > DedupSNPConfirmed_ResistomeResults (null) [100%] 1 of 1, failed: 1 ✔ [1e/8779a5] NOTE: Missing output file(s) S3_test_rgi_perfect_hits.csv expected by process DedupSNPconfirmation (S3_test) -- Error is ignored [f8/27c008] NOTE: Process DedupSNPConfirmed_ResistomeResults (null) terminated with an error exit status (2) -- Error is ignored [fd/ca80a7] NOTE: Missing output file(s) S3_test_rgi_perfect_hits.csv expected by process SNPconfirmation (S3_test) -- Error is ignored [9e/211eb5] NOTE: Process Confirmed_ResistomeResults (null) terminated with an error exit status (2) -- Error is ignored Completed at: 29-Jan-2021 09:24:20 Duration : 3m 36s CPU hours : 0.2 (0.9% failed) Succeeded : 42 Ignored : 8 Failed : 8

[chaichai9522]

did you fix your problem? how did you install Singularity container?