python error (probably)

Hi, Mr., thanks for the last answer, you were really kind!, it seems that now i have another issue. I reinstalled it using source again, from this step "conda env create -f environment_linux.yml"

unfortunately, this is what i get:

(ggc_env) [mdavid@soroban IMSAR217cc11]$ nohup ggcaller --refs input.txt --threads 50 & [1] 356615 (ggc_env) [mdavid@soroban IMSAR217cc11]$ nohup: ignoring input and appending output to ‘nohup.out’ jobs [1]+ Running nohup ggcaller --refs input.txt --threads 50 & (ggc_env) [mdavid@soroban IMSAR217cc11]$ cat nohup.out Building coloured compacted DBG... (ggc_env) [mdavid@soroban IMSAR217cc11]$ cat nohup.out Building coloured compacted DBG... (ggc_env) [mdavid@soroban IMSAR217cc11]$ ls -lh total 479M -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 113198_DE14151_PacBio.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 113205_DE14168_PacBio.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 122164_18_122_hybrid.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 122165_18_62_hybrid.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 2290_M7124.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 31317_NM3686.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 31318_NM3682.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 31319_M10208.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 31332_NM3683.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36448_2636.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36449_2639.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36450_2644.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36451_2652.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36452_2664.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36453_2665.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36454_1982.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36455_1983.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36456_1984.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36457_1985.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36458_1986.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36459_1987.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36461_2560.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36462_1981.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36463_2380.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 36689_M25543.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36848_2593.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 36849_2585.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39628_82_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39629_83_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39630_111_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39632_171_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39633_179_15.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 39634_583_15.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 39638_666_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39641_1010_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39645_1064_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39647_1082_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39649_1083_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39650_1090_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39651_1096_15.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 39775_1658_15.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 39781_1847_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39791_2029_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39795_2099_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39797_2143_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39798_2146_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39812_2749_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39827_3833_15.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39836_M03473.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39837_M05730.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39842_M04874.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39845_M03564.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39846_M05451.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39847_M05831.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39849_M05731.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39850_M05732.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39851_M05733.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39855_M05737.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39859_M05738.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39861_M00601.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39865_M21374.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39866_M21427.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39867_M21428.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39870_M21716.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39871_M21717.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39878_M26925.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39879_M26926.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39880_M26919.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39882_M25670.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39883_M26294.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39884_M26295.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39889_M26949.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39892_M26017.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39893_M26263.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39896_M27267.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39898_M26089.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39899_M25964.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39900_M26087.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39901_M26088.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 39903_M26416.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 41785_2838.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 41787_0393_93.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 42848_M26242.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45110_M23151.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45113_M23599.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45114_M23600.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45115_M23677.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45118_M25165.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45119_M25241.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45120_M25244.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45121_M25633.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45122_M25635.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45124_M25683.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45125_M25684.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45127_M25688.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45128_M25874.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45133_M26021.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45138_M26093.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45139_M26247.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45157_M27458.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45158_M27459.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45159_M27471.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45161_M27885.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45167_M28971.fasta -rw-r--r-- 1 mdavid bioren 2,0M nov 21 19:58 45168_M28979.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45172_M29225.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45173_M29276.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45181_M37929.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45184_M38252.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45185_M38355.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45187_M38738.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45188_M38741.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45189_M38742.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 45190_M38917.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 45893_L91543.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46977_DE8555.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46979_M07149.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46980_M07161.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46981_M07162.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 46982_M08000.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 46983_M08001.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 46984_M09261.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46985_M12752.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 46986_M22191.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46987_M22718.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46988_M22722.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46989_M22740.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 46991_M22748.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46992_M22759.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46993_M22769.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46994_M22772.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 46996_M22801.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47003_M23413.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47005_M25070.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47006_M25087.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47007_M25419.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47008_M25438.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47009_M25472.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47010_M25476.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47011_M27559.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47012_WUE2121.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47233_CNM3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47234_M40240.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 47235_M21273.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 49271_NM3.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 49272_NM4.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57572_11_590_251.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57573_12_590_208.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57574_14_590_159.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57575_14_590_627.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57577_NEIS_15_193.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57578_NEIS_15_198.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57579_NEIS_15_215.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57580_NEIS_15_236.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57582_NEIS_16_92.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57583_NEIS_16_306.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 57584_NEIS_16_579.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 58230_M25462.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 58253_M25456.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 58271_M25459.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 58300_M25439.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 58322_M25474.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 58347_M25073.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 58348_M25074.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 62972_M22718.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 62984_DW8555.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 62986_WUE2121.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 62987_3683.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 62988_M07149.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 62989_M07162.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 62991_M25459.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 698_FAM18.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81898_11_251_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81899_12_208_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81900_14_159_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81901_14_627_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81902_15_123_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81904_15_198_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81905_15_215_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81907_16_7_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81908_16_92_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81909_16_306_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 81910_16_579_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82040_11_251_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82041_12_208_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82043_14_627_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82044_15_123_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82045_15_193_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82046_15_198_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82048_15_236_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82049_16_7_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82050_16_92_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82051_16_306_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82052_16_579_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82218_14_159_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82219_NEIS_15_123.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82220_15_193_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82221_15_215_3.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82222_15_236_2.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 82224_NEIS_16_7.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 84413_DL20404.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 85163_M22803.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95884_11_251.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95885_12_208.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95886_14_159.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95887_14_627.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95888_15_123.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95889_15_193.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95890_15_198.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95891_15_215.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95892_15_236.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95893_16_7.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95894_16_92.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95895_16_306.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 95896_16_579.fasta -rw-r--r-- 1 mdavid bioren 2,2M nov 21 19:58 97476_M23405.fasta -rw-r--r-- 1 mdavid bioren 2,1M nov 21 19:58 97883_Nmiss3092.fasta drwxr-xr-x 2 mdavid bioren 10 nov 25 02:09 ggCaller_output -rw-r--r-- 1 mdavid bioren 4,8M nov 25 02:10 input.color.bfg -rw-r--r-- 1 mdavid bioren 19M nov 25 02:10 input.gfa -rw-r--r-- 1 mdavid bioren 14K nov 25 02:06 input.txt -rw------- 1 mdavid bioren 72 nov 25 02:10 nohup.out (ggc_env) [mdavid@soroban IMSAR217cc11]$ cat nohup.out Building coloured compacted DBG... Generating graph stop codon index... Mapping contigs to graph... Downloading databases... Traceback (most recent call last): File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/urllib/request.py", line 1346, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/http/client.py", line 1285, in request self._send_request(method, url, body, headers, encode_chunked) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/http/client.py", line 1331, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/http/client.py", line 1280, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/http/client.py", line 1040, in _send_output self.send(msg) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/http/client.py", line 980, in send self.connect() File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/http/client.py", line 1454, in connect self.sock = self._context.wrap_socket(self.sock, File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/ssl.py", line 501, in wrap_socket return self.sslsocket_class._create( File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/ssl.py", line 1074, in _create self.do_handshake() File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/ssl.py", line 1343, in do_handshake self._sslobj.do_handshake() ConnectionResetError: [Errno 104] Connection reset by peer

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/bioren/mdavid/.conda/envs/ggc_env/bin/ggcaller", line 33, in sys.exit(load_entry_point('ggCaller==1.3.4', 'console_scripts', 'ggcaller')()) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/ggCaller/main.py", line 436, in main db_dir = download_db() File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/models/main.py", line 15, in download_db filename = wget.download(url, out=module_dir) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/site-packages/wget.py", line 526, in download (tmpfile, headers) = ulib.urlretrieve(binurl, tmpfile, callback) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/urllib/request.py", line 239, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/urllib/request.py", line 214, in urlopen return opener.open(url, data, timeout) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/urllib/request.py", line 517, in open response = self._open(req, data) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/urllib/request.py", line 534, in _open result = self._call_chain(self.handle_open, protocol, protocol + File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/urllib/request.py", line 494, in _call_chain result = func(*args) File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/urllib/request.py", line 1389, in https_open return self.do_open(http.client.HTTPSConnection, req, File "/home/bioren/mdavid/.conda/envs/ggc_env/lib/python3.9/urllib/request.py", line 1349, in do_open raise URLError(err) urllib.error.URLError: <urlopen error [Errno 104] Connection reset by peer> [1]+ Exit 1 nohup ggcaller --refs input.txt --threads 50

Sorry for being a pain in the ass.

Cheers

bacpop / ggCaller

python error (probably) #16