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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
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Centrifuge Classifying Reads, but the Report is Empty #279

Closed echolley31 closed 5 months ago

echolley31 commented 5 months ago

Hi all, I've been trying to run Centrifuge for metagenomic analysis. It appears to be classifying reads, but when it comes to the output report, the report is empty. I have my code I'm using and the output files below. Please let me know what I am doing wrong/how to fix this? Thanks!

My input line:

centrifuge --threads 32 --met-stderr -x p+h+v -1 /sciclone/scr10/echolley/igem/myco_meta/fastqs/trimmed/M07CI1_val_1.fq.gz -2 /sciclone/scr10/echolley/igem/myco_meta/fastqs/trimmed/M07CI1_val_2.fq.gz -S test1 --report-file test1_report Output:

52 [bora] head test1 readID seqID taxID score 2ndBestScore hitLength queryLength numMatches LH00260:52:2255MVLT4:5:1101:29736:1042 unclassified 0 0 0 0 70 1 LH00260:52:2255MVLT4:5:1101:30011:1042 unclassified 0 0 0 0 300 1 LH00260:52:2255MVLT4:5:1101:31127:1042 unclassified 0 0 0 0 246 1 LH00260:52:2255MVLT4:5:1101:32309:1042 unclassified 0 0 0 0 194 1 LH00260:52:2255MVLT4:5:1101:33231:1042 unclassified 0 0 0 0 300 1 LH00260:52:2255MVLT4:5:1101:33053:1042 unclassified 0 0 0 0 212 1 LH00260:52:2255MVLT4:5:1101:34688:1042 unclassified 0 0 0 0 254 1 LH00260:52:2255MVLT4:5:1101:35481:1042 unclassified 0 0 0 0 288 1 LH00260:52:2255MVLT4:5:1101:33345:1042 unclassified 0 0 0 0 218 1 Report:

53 [bora] head test1_report name taxID taxRank genomeSize numReads numUniqueReads abundance

mourisl commented 5 months ago

Are all the reads unclassified in test1?

echolley31 commented 5 months ago

No, there's plenty of sequences that are classified it appears.

LH00260:52:2255MVLT4:5:1102:51884:14363 NC_021658.1 1254432 128 0 46 96 1 LH00260:52:2255MVLT4:5:1102:50120:14363 NC_010572.1 455632 64 0 23 230 1 LH00260:52:2255MVLT4:5:1102:46608:14363 NZ_CP011367.1 106634 1225 81 50 301 1 LH00260:52:2255MVLT4:5:1102:51690:14363 unclassified 0 0 0 0 302 1 LH00260:52:2255MVLT4:5:1102:2319:14377 unclassified 0 0 0 0 301 1 LH00260:52:2255MVLT4:5:1102:6414:14377 unclassified 0 0 0 0 220 1 LH00260:52:2255MVLT4:5:1102:6478:14377 unclassified 0 0 0 0 301 1 LH00260:52:2255MVLT4:5:1102:7547:14377 unclassified 0 0 0 0 301 1 LH00260:52:2255MVLT4:5:1102:8938:14377 unclassified 0 0 0 0 240 1 LH00260:52:2255MVLT4:5:1102:8372:14377 unclassified 0 0 0 0 302 1 LH00260:52:2255MVLT4:5:1102:9133:14377 unclassified 0 0 0 0 212 1 LH00260:52:2255MVLT4:5:1102:10055:14377 unclassified 0 0 0 0 184 1 LH00260:52:2255MVLT4:5:1102:10120:14377 unclassified 0 0 0 0 128 1 LH00260:52:2255MVLT4:5:1102:10152:14377 unclassified 0 0 0 0 278 1 LH00260:52:2255MVLT4:5:1102:10848:14377 unclassified 0 0 0 0 228 1 LH00260:52:2255MVLT4:5:1102:10719:14377 NZ_CP014352.1 1748 128 128 46 210 3 LH00260:52:2255MVLT4:5:1102:10719:14377 NC_019395.1 1171373 128 128 46 210 3 LH00260:52:2255MVLT4:5:1102:10719:14377 NZ_CP015970.1 1748 128 128 46 210 3 LH00260:52:2255MVLT4:5:1102:12159:14377 NZ_LN997841.1 1752 162 0 48 136 1 LH00260:52:2255MVLT4:5:1102:13324:14377 unclassified 0 0 0 0 212 1 LH00260:52:2255MVLT4:5:1102:14457:14377 unclassified 0 0 0 0 302 1 LH00260:52:2255MVLT4:5:1102:17630:14377 unclassified 0 0 0 0 146 1 LH00260:52:2255MVLT4:5:1102:14862:14377 NZ_CP015371.1 93220 64 64 23 300 2 LH00260:52:2255MVLT4:5:1102:14862:14377 NZ_CP007506.3 93220 64 64 23 300 2 LH00260:52:2255MVLT4:5:1102:17193:14377 unclassified 0 0 0 0 202 1 LH00260:52:2255MVLT4:5:1102:16319:14377 unclassified 0 0 0 0 301 1 LH00260:52:2255MVLT4:5:1102:19167:14377 unclassified 0 0 0 0 302 1 LH00260:52:2255MVLT4:5:1102:20818:14377 unclassified 0 0 0 0 294 1 LH00260:52:2255MVLT4:5:1102:20413:14377 NZ_CP013997.1 76759 128 128 46 302 2 LH00260:52:2255MVLT4:5:1102:20413:14377 NZ_CP009747.1 157782 128 128 46 302 2 LH00260:52:2255MVLT4:5:1102:24476:14377 unclassified 0 0 0 0 122 1

echolley31 commented 5 months ago

Update: I realized that it may have been because my input file was gunzipped. I have tried unzipping the files and that appeared to have an output that was predicted.