Broken files on Hilbert

[deyazoubi]

a list of open and closed To-Dos: recover these files from old backups/ reprocess broken files

• [x] transfer our Backup from NAS to the HCP, extract it and replace the below-listed file of run 191211_SN737_0487_BCDVUBACXX(transferd) and 190107_SN737_0456_ACCDC1ACXX
• [x] KB0046_m_S4_L001_R1_001.fastq.gz path is 025_demultiplex/160315_SN737_0379_AC8NBPACXX/part_1/Keimbahn/
• [x] mRJ_366_N_S4_L002_R2_001.fastq.gz (Intermediate step no problem) path is 025_demultiplex/191211_SN737_0487_BCDVUBACXX/part_2/Maus_Hauer/
• [x] KB0046_m_L001_R1_001.fastq.gz(Intermediate step no problem) path is 026_join_demultiplex/160315_SN737_0379_AC8NBPACXX/Keimbahn/
• [x] mRJ_366_N_L002_R2_001.fastq.gz (Intermediate step no problem) path is 026_join_demultiplex/191211_SN737_0487_BCDVUBACXX/Maus_Hauer/
• [x] 060_map/Maus_Hauer/mRJ_318_T.srt.bam(Intermediate step no problem)
• [x] 075_gatk_IndelRealigner/Keimbahn/KB0294_f.reAl.nodup.srt.bam
• [ ] Raw_Illumina/160112_SN737_0374_AC8D03ACXX/Data/Intensities/BaseCalls/L003/C67.1/s_3_2108.bcl.gz
• [ ] Raw_Illumina/160922_SN737_0394_AC92ALACXX/Data/Intensities/BaseCalls/L003/C184.1/s_3_1205.bcl.gz
• [ ] Raw_Illumina/161214_SN737_0402_BCA4C4ACXX/Data/Intensities/BaseCalls/L002/C99.1/s_2_2215.bcl.gz
• [ ] Raw_Illumina/161221_SN737_0403_ACA2GBACXX/Data/Intensities/BaseCalls/L004/C13.1/s_4_1309.bcl.gz
• [ ] Raw_Illumina/170201_SN737_0405_BCA4AUACXX/Data/Intensities/BaseCalls/L002/C151.1/s_2_2210.bcl.gz
• [ ] Raw_Illumina/170217_SN737_0406_ACA6UEACXX/Data/Intensities/BaseCalls/L002/C42.1/s_2_2104.bcl.gz
• [ ] Raw_Illumina/170217_SN737_0406_ACA6UEACXX/Data/Intensities/BaseCalls/L003/C13.1/s_3_1109.bcl.gz
• [ ] Raw_Illumina/170302_SN737_0408_ACA6TRACXX/Data/Intensities/BaseCalls/L002/C111.1/s_2_2211.bcl.gz
• [ ] Raw_Illumina/180316_SN737_0434_BCBJGNACXX/Data/Intensities/BaseCalls/L005/C11.1/s_5_2212.bcl.gz
• [ ] Raw_Illumina/180316_SN737_0434_BCBJGNACXX/Data/Intensities/BaseCalls/L005/C70.1/s_5_2213.bcl.gz
• [ ] Raw_Illumina/180316_SN737_0434_BCBJGNACXX/Data/Intensities/BaseCalls/L008/C139.1/s_8_2104.bcl.gz
• [ ] Raw_Illumina/180316_SN737_0434_BCBJGNACXX/Data/Intensities/BaseCalls/L008/C141.1/s_8_2104.bcl.gz
• [ ] Raw_Illumina/180614_SN737_0438_BCC7MCACXX/Data/Intensities/BaseCalls/L002/C33.1/s_2_2315.bcl.gz
• [ ] Raw_Illumina/180614_SN737_0438_BCC7MCACXX/Data/Intensities/BaseCalls/L002/C34.1/s_2_1116.bcl.gz
• [ ] Raw_Illumina/180614_SN737_0438_BCC7MCACXX/Thumbnail_Images/L002/C169.1/s_2_1116_T.jpg
• [ ] Raw_Illumina/180614_SN737_0438_BCC7MCACXX/Thumbnail_Images/L002/C169.1/s_2_1201_A.jpg
• [ ] Raw_Illumina/180614_SN737_0438_BCC7MCACXX/Thumbnail_Images/L002/C169.1/s_2_1201_C.jpg
• [ ] Raw_Illumina/181210_SN737_0454_ACC8NFACXX/Data/Intensities/BaseCalls/L008/C189.1/s_8_1214.bcl.gz
• [ ] Raw_Illumina/181210_SN737_0454_ACC8NFACXX/Data/Intensities/BaseCalls/L008/C189.1/s_8_1216.bcl.gz
• [ ] Raw_Illumina/181210_SN737_0454_ACC8NFACXX/Data/Intensities/BaseCalls/L008/C193.1/s_8_1301.bcl.gz
• [ ] Raw_Illumina/181210_SN737_0455_BCCDF3ACXX/Data/Intensities/BaseCalls/L006/C98.1/s_6_1311.bcl.gz
• [ ] Raw_Illumina/190107_SN737_0456_ACCDC1ACXX/Data/Intensities/BaseCalls/L007/C62.1/s_7_1315.bcl.gz
• [ ] Raw_Illumina/190221_SN737_0460_ACCPH3ACXX/Thumbnail_Images/L005/C60.1/ccph3acxx_c060_l5_t001_top_s2_a.jpg
• [ ] Raw_Illumina/190327_SN737_0462_ACCW9LACXX/Data/Intensities/BaseCalls/L003/C82.1/s_3_1313.bcl.gz
• [ ] Raw_Illumina/190327_SN737_0462_ACCW9LACXX/Data/Intensities/BaseCalls/L003/C82.1/s_3_1316.bcl.gz
• [ ] Intermediate/035_rejoin_samples/Keimbahn/KB0019_m_R2.fastq.gz
• [x] Intermediate/060_map/Keimbahn/KB0244_c.srt.bam(Intermediate step no problem)
• [x] Intermediate/061_unmap/Maus_Hauer/229C.bwamem(Intermediate step no problem)
• [x] Intermediate/065_remove_pcr_duplicates/Alps/ALPS_35b.nodup.srt.bam(Intermediate step no problem)
• [x] Intermediate/065_remove_pcr_duplicates/Keimbahn/KB0087_m.nodup.srt.bam(Intermediate step no problem)
• [ ] Intermediate/085_gatk_PrintReads/Keimbahn/KB0091_m.reCal.reAl.nodup.srt.bam
• [x] Intermediate/025_demultiplex/160315_SN737_0379_AC8NBPACXX/part_1/Keimbahn/KB0046_m_S4_L001_R1_001.fastq.gz(Intermediate step no problem)
• [x] Intermediate/025_demultiplex/191211_SN737_0487_BCDVUBACXX/part_2/Maus_Hauer/mRJ_366_N_S4_L002_R2_001.fastq.gz(Intermediate step no problem)
• [x] Intermediate/026_join_demultiplex/160315_SN737_0379_AC8NBPACXX/Keimbahn/KB0046_m_L001_R1_001.fastq.gz(Intermediate step no problem)
• [x] Intermediate/026_join_demultiplex/191211_SN737_0487_BCDVUBACXX/Maus_Hauer/mRJ_366_N_L002_R2_001.fastq.gz(Intermediate step no problem)
• [ ] Intermediate/060_map/Maus_Hauer/mRJ_318_T.srt.bam(Intermediate step no problem)
• [x] Intermediate/075_gatk_IndelRealigner/Keimbahn/KB0294_f.reAl.nodup.srt.bam(Intermediate step no problem)