Timmywang1
commented
4 years ago Open Timmywang1 opened 4 years ago
Timmywang1
commented
4 years ago 
ursky
commented
4 years ago Can you provide the contents of clean.S1.quant.counts and the other files? Its strange there is no stderr merrage,,,
Timmywang1
commented
4 years ago head -n 40 clean.S1.quant.counts
transcript count
k141_1 0.0
k141_2 0.0
k141_3 0.474976
k141_4 0.0
k141_5 0.0
k141_6 0.0
k141_7 0.378531
k141_8 0.122853
k141_9 0.0
k141_10 0.0
k141_11 0.0
k141_12 0.0
k141_13 0.287786
k141_14 0.0
k141_15 0.0
k141_16 0.622564
k141_17 0.344229
k141_18 0.355191
k141_19 0.098537
k141_20 0.357389
k141_21 0.449514
k141_23 0.073421
k141_24 0.172549
k141_25 1.366322
k141_26 0.17674
k141_27 0.0
k141_28 0.0
k141_29 0.0
k141_30 0.0
k141_31 0.633335
k141_32 0.0
k141_33 0.0
k141_34 0.129662
k141_35 0.470713
k141_36 0.0
k141_37 0.383072
k141_38 0.355191
k141_39 0.216108
k141_40 0.490431Thank you for your help!
ursky
commented
4 years ago Can you go in and investidate what the exact component is that failed? This is the exact script that is failing in the pipeline:
bin/metawrap-scripts/split_salmon_out_into_bins.py /share/home/binhaow/metagenomedata4/QUANT_BINS3/quant_files/ /share/home/binhaow/metagenomedata3/BIN_REFINEMENT3/metawrap_60_10_bins/ /share/home/binhaow/metagenomedata3/ASSEMBLY3/megahit/final.contigs1_5.fa > /share/home/binhaow/metagenomedata4/QUANT_BINS3/bin_abundance_table.tab
Basically, it takes in the contents of QUANT_BINS3/quant_files/. Can you check if anything looks suspicious? And what error the command throws?
Timmywang1
commented
4 years ago When I run the command--"bin/metawrap-scripts/split_salmon_out_into_bins.py ", the contents in the table are as follows:
None of the contigs/scaffolds in the -a metagenomic assembly file were present in the bin files. Please make sure that the bins and total assembly have the exact same bins. One cause for this could be that you reassembled the bins, disrupring the contig naming. If you do not have the original total metagenomic assembly file, then you could not provide the -a option at all (but this is not ideal for abundance estimation).
ursky
commented
4 years ago Ah. There's your answer right there. The contigs in the assembly you provided did not match those in the bins you provided. Double-check your inputs by looking at the contig names, and re-run once you find what was wrong. You could also just not provide the assembly, which would make the results slightly less accurate.
Timmywang1
commented
4 years ago hello, I have some problems. I have 5 samples. I don’t want to know the average abundance. I want to know the abundance in each sample. How should I set it?
<metawrap quant_bins -b metawrap_60_10_bins/ -t 20 -o QUANT_BINS3 -a final_assembly.fasta CLEAN_READS3/clean.S1_1.fastq CLEAN_READS3/clean.S1_2.fastq CLEAN_READS3/clean.S2_1.fastq CLEAN_READS3/clean.S2_2.fastq CLEAN_READS3/clean.S3_1.fastq CLEAN_READS3/clean.S3_2.fastq CLEAN_READS3/clean.S4_1.fastq CLEAN_READS3/clean.S4_2.fastq CLEAN_READS3/clean.S5_1.fastq CLEAN_READS3/clean.S5_2.fastq>
------------------------------------------------------------------------------------------------------------------------
----- There were 5 samples detected. Making abundance table! -----
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----- Average bin abundance table stored in QUANT_BINS3/abundance_table.tab -----
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########################################################################################################################
##### MAKING GENOME ABUNDANCE HEATMAP WITH SEABORN #####
########################################################################################################################
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----- making heatmap with Seaborn -----
------------------------------------------------------------------------------------------------------------------------
loading libs...
loading abundance data...
drawing clustermap...
Traceback (most recent call last):
File "/share/home/binhaow/anaconda2/envs/metawrap/bin/metawrap-scripts/make_heatmap.py", line 75, in <module>
draw_clustermap(df, lut)
File "/share/home/binhaow/anaconda2/envs/metawrap/bin/metawrap-scripts/make_heatmap.py", line 58, in draw_clustermap
g = sns.clustermap(df, figsize=(14,8), col_cluster=True, yticklabels=True, cmap="magma")
File "/share/home/binhaow/anaconda2/envs/metawrap/lib/python2.7/site-packages/seaborn/matrix.py", line 1301, in clustermap
**kwargs)
File "/share/home/binhaow/anaconda2/envs/metawrap/lib/python2.7/site-packages/seaborn/matrix.py", line 1131, in plot
row_linkage=row_linkage, col_linkage=col_linkage)
File "/share/home/binhaow/anaconda2/envs/metawrap/lib/python2.7/site-packages/seaborn/matrix.py", line 1032, in plot_dendrograms
axis=1, ax=self.ax_col_dendrogram, linkage=col_linkage)
File "/share/home/binhaow/anaconda2/envs/metawrap/lib/python2.7/site-packages/seaborn/matrix.py", line 746, in dendrogram
label=label, rotate=rotate)
File "/share/home/binhaow/anaconda2/envs/metawrap/lib/python2.7/site-packages/seaborn/matrix.py", line 564, in __init__
self.linkage = self.calculated_linkage
File "/share/home/binhaow/anaconda2/envs/metawrap/lib/python2.7/site-packages/seaborn/matrix.py", line 628, in calculated_linkage
return self._calculate_linkage_scipy()
File "/share/home/binhaow/anaconda2/envs/metawrap/lib/python2.7/site-packages/seaborn/matrix.py", line 603, in _calculate_linkage_scipy
metric=self.metric)
File "/share/home/binhaow/anaconda2/envs/metawrap/lib/python2.7/site-packages/scipy/cluster/hierarchy.py", line 716, in linkage
n = int(distance.num_obs_y(y))
File "/share/home/binhaow/anaconda2/envs/metawrap/lib/python2.7/site-packages/scipy/spatial/distance.py", line 2276, in num_obs_y
raise ValueError("The number of observations cannot be determined on "
ValueError: The number of observations cannot be determined on an empty distance matrix.
************************************************************************************************************************
***** something went wrong with making the heatmap. Exiting... *****
************************************************************************************************************************It would be helpful to have the entire output (strout + stderr) to daignose this.