Question on ffq [DOIS] - Githubissues

Greetings ffq developers,

Could anyone help explain a bit why my first attempt to fetch the accession information from one paper (https://doi.org/10.1016/j.cell.2023.01.034) fails, while my second attempt for another paper (https://doi.org/10.1093/nar/gkac908) is successful? The commands and corresponding outputs for 2 studies are shared here. In either situation, ffq 0.3.0 and Python 3.11.1 are used.

In each attempt, the similar warning messages pop up in my terminal: "WARNING Failed to parse sample information from ENA XML. Falling back to ENA search...". For the first study, there is no output file in json format. However, for the second study, even I meet this sort of warning message of SRX8785942, the output file nar.json contains the information of SRX8785942, as you see below.

[2023-08-19 16:10:13,676] INFO Parsing Experiment SRX8785942 [2023-08-19 16:10:13,681] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:14,088] WARNING There are 0 runs for SRX8785942

" "experiments": { "SRX8785942": { "accession": "SRX8785942", "title": "Illumina NovaSeq 6000 paired end sequencing; GSM4681765: Breast cancer cells - MCF7 CL; Homo sapiens; RNA-Seq", "platform": "ILLUMINA", "instrument": "Illumina NovaSeq 6000", "runs": {} }"

Look forward to learning from your insights. I really appreciate your help in advance.

ffq -o ./json_file/cell.json 10.1016/j.cell.2023.01.034 --verbose

Output: [2023-08-19 15:40:47,871] DEBUG Printing verbose output [2023-08-19 15:40:47,871] DEBUG Namespace(IDs=['10.1016/j.cell.2023.01.034'], o=None, t=None, l=None, ftp=False, aws=False, gcp=False, ncbi=False, split=False, verbose=True) [2023-08-19 15:40:47,871] WARNING Searching by DOI may result in missing information. [2023-08-19 15:40:47,871] INFO Searching for DOI '10.1016/J.CELL.2023.01.034' [2023-08-19 15:40:47,978] INFO Searching for Study SRP with title 'Cell lineage-specific mitochondrial resilience during mammalian organogenesis' [2023-08-19 15:40:48,510] INFO Found 2 studies that match this title: SRP370066, SRP400925 [2023-08-19 15:40:48,511] INFO Parsing Study SRP370066 [2023-08-19 15:40:48,936] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:48,937] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:48,939] INFO Getting Sample for SRP370066 [2023-08-19 15:40:53,327] WARNING There are 5 samples for SRP370066 [2023-08-19 15:40:53,327] INFO Parsing sample SRS12598636 [2023-08-19 15:40:53,741] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:53,742] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:53,745] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:40:54,462] INFO Getting Experiment for SRS12598636 [2023-08-19 15:40:54,462] INFO Parsing Experiment SRX14843696 [2023-08-19 15:40:54,882] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:54,883] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:54,886] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:40:55,573] WARNING There is 1 run for SRX14843696 [2023-08-19 15:40:55,574] INFO Parsing run SRR18743675 [2023-08-19 15:40:55,999] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:55,999] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:57,846] INFO Parsing sample SRS12598635 [2023-08-19 15:40:58,260] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:58,260] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:58,263] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:40:58,670] INFO Getting Experiment for SRS12598635 [2023-08-19 15:40:58,670] INFO Parsing Experiment SRX14843695 [2023-08-19 15:40:59,088] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:59,089] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:59,093] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:40:59,501] WARNING There is 1 run for SRX14843695 [2023-08-19 15:40:59,501] INFO Parsing run SRR18743676 [2023-08-19 15:40:59,903] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:40:59,903] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:02,002] INFO Parsing sample SRS12598634 [2023-08-19 15:41:02,413] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:02,413] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:02,416] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:02,952] INFO Getting Experiment for SRS12598634 [2023-08-19 15:41:02,952] INFO Parsing Experiment SRX14843694 [2023-08-19 15:41:03,361] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:03,362] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:03,365] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:03,780] WARNING There is 1 run for SRX14843694 [2023-08-19 15:41:03,780] INFO Parsing run SRR18743677 [2023-08-19 15:41:04,187] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:04,187] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:07,105] INFO Parsing sample SRS12598633 [2023-08-19 15:41:07,512] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:07,512] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:07,515] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:07,921] INFO Getting Experiment for SRS12598633 [2023-08-19 15:41:07,921] INFO Parsing Experiment SRX14843693 [2023-08-19 15:41:08,331] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:08,332] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:08,336] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:08,744] WARNING There is 1 run for SRX14843693 [2023-08-19 15:41:08,745] INFO Parsing run SRR18743678 [2023-08-19 15:41:09,147] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:09,147] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:11,117] INFO Parsing sample SRS12598637 [2023-08-19 15:41:11,532] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:11,532] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:11,535] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:12,129] INFO Getting Experiment for SRS12598637 [2023-08-19 15:41:12,129] INFO Parsing Experiment SRX14843697 [2023-08-19 15:41:12,544] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:12,545] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:12,548] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:12,956] WARNING There is 1 run for SRX14843697 [2023-08-19 15:41:12,956] INFO Parsing run SRR18743674 [2023-08-19 15:41:13,365] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:13,366] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:15,265] INFO Parsing Study SRP400925 [2023-08-19 15:41:15,683] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:15,684] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:15,685] INFO Getting Sample for SRP400925 [2023-08-19 15:41:30,185] WARNING There are 20 samples for SRP400925 [2023-08-19 15:41:30,185] INFO Parsing sample SRS15319024 [2023-08-19 15:41:30,626] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:30,626] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:30,631] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:31,051] INFO Getting Experiment for SRS15319024 [2023-08-19 15:41:31,052] INFO Parsing Experiment SRX17793201 [2023-08-19 15:41:31,487] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:31,487] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:31,492] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:32,709] WARNING There are 2 runs for SRX17793201 [2023-08-19 15:41:32,709] INFO Parsing run SRR21799208 [2023-08-19 15:41:33,141] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:33,142] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:35,187] INFO Parsing run SRR21799209 [2023-08-19 15:41:35,614] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:35,615] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:37,563] INFO Parsing sample SRS15319023 [2023-08-19 15:41:37,991] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:37,992] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:37,997] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:38,414] INFO Getting Experiment for SRS15319023 [2023-08-19 15:41:38,415] INFO Parsing Experiment SRX17793200 [2023-08-19 15:41:38,839] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:38,840] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:38,847] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:39,272] WARNING There are 2 runs for SRX17793200 [2023-08-19 15:41:39,272] INFO Parsing run SRR21799210 [2023-08-19 15:41:39,693] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:39,694] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:41,682] INFO Parsing run SRR21799211 [2023-08-19 15:41:42,102] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:42,102] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:44,049] INFO Parsing sample SRS15319023 [2023-08-19 15:41:44,055] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:44,055] INFO Getting Experiment for SRS15319023 [2023-08-19 15:41:44,055] INFO Parsing Experiment SRX17793200 [2023-08-19 15:41:44,059] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:44,060] WARNING There are 2 runs for SRX17793200 [2023-08-19 15:41:44,060] INFO Parsing run SRR21799210 [2023-08-19 15:41:44,317] INFO Parsing run SRR21799211 [2023-08-19 15:41:44,591] INFO Parsing sample SRS15319020 [2023-08-19 15:41:45,020] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:45,021] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:45,025] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:45,438] INFO Getting Experiment for SRS15319020 [2023-08-19 15:41:45,438] INFO Parsing Experiment SRX17793197 [2023-08-19 15:41:45,871] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:45,871] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:45,878] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:46,292] WARNING There are 2 runs for SRX17793197 [2023-08-19 15:41:46,292] INFO Parsing run SRR21799216 [2023-08-19 15:41:46,714] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:46,715] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:48,669] INFO Parsing run SRR21799217 [2023-08-19 15:41:49,102] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:49,103] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:51,084] INFO Parsing sample SRS15319017 [2023-08-19 15:41:51,514] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:51,515] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:51,521] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:51,944] INFO Getting Experiment for SRS15319017 [2023-08-19 15:41:51,944] INFO Parsing Experiment SRX17793194 [2023-08-19 15:41:52,365] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:52,366] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:52,371] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:52,791] WARNING There are 2 runs for SRX17793194 [2023-08-19 15:41:52,791] INFO Parsing run SRR21799222 [2023-08-19 15:41:53,222] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:53,223] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:55,341] INFO Parsing run SRR21799223 [2023-08-19 15:41:55,761] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:55,761] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:57,729] INFO Parsing sample SRS15319017 [2023-08-19 15:41:57,735] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:57,735] INFO Getting Experiment for SRS15319017 [2023-08-19 15:41:57,735] INFO Parsing Experiment SRX17793194 [2023-08-19 15:41:57,740] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:57,740] WARNING There are 2 runs for SRX17793194 [2023-08-19 15:41:57,740] INFO Parsing run SRR21799222 [2023-08-19 15:41:58,001] INFO Parsing run SRR21799223 [2023-08-19 15:41:58,289] INFO Parsing sample SRS15319016 [2023-08-19 15:41:58,714] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:58,715] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:58,725] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:59,142] INFO Getting Experiment for SRS15319016 [2023-08-19 15:41:59,142] INFO Parsing Experiment SRX17793193 [2023-08-19 15:41:59,570] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:59,570] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:41:59,581] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:41:59,996] WARNING There are 2 runs for SRX17793193 [2023-08-19 15:41:59,996] INFO Parsing run SRR21799225 [2023-08-19 15:42:00,427] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:00,427] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:02,381] INFO Parsing run SRR21799224 [2023-08-19 15:42:02,808] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:02,809] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:04,780] INFO Parsing sample SRS15319022 [2023-08-19 15:42:05,203] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:05,203] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:05,208] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:05,746] INFO Getting Experiment for SRS15319022 [2023-08-19 15:42:05,746] INFO Parsing Experiment SRX17793199 [2023-08-19 15:42:06,180] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:06,181] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:06,188] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:06,610] WARNING There are 2 runs for SRX17793199 [2023-08-19 15:42:06,611] INFO Parsing run SRR21799212 [2023-08-19 15:42:07,031] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:07,032] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:08,995] INFO Parsing run SRR21799213 [2023-08-19 15:42:09,423] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:09,425] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:11,391] INFO Parsing sample SRS15319021 [2023-08-19 15:42:11,822] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:11,823] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:11,828] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:12,243] INFO Getting Experiment for SRS15319021 [2023-08-19 15:42:12,243] INFO Parsing Experiment SRX17793198 [2023-08-19 15:42:12,667] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:12,669] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:12,674] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:13,114] WARNING There are 2 runs for SRX17793198 [2023-08-19 15:42:13,114] INFO Parsing run SRR21799215 [2023-08-19 15:42:13,533] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:13,534] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:15,519] INFO Parsing run SRR21799214 [2023-08-19 15:42:15,939] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:15,940] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:17,899] INFO Parsing sample SRS15319020 [2023-08-19 15:42:17,906] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:17,906] INFO Getting Experiment for SRS15319020 [2023-08-19 15:42:17,907] INFO Parsing Experiment SRX17793197 [2023-08-19 15:42:17,912] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:17,912] WARNING There are 2 runs for SRX17793197 [2023-08-19 15:42:17,912] INFO Parsing run SRR21799216 [2023-08-19 15:42:18,174] INFO Parsing run SRR21799217 [2023-08-19 15:42:18,437] INFO Parsing sample SRS15319018 [2023-08-19 15:42:18,847] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:18,848] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:18,852] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:19,265] INFO Getting Experiment for SRS15319018 [2023-08-19 15:42:19,265] INFO Parsing Experiment SRX17793195 [2023-08-19 15:42:19,688] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:19,688] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:19,692] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:20,100] WARNING There are 2 runs for SRX17793195 [2023-08-19 15:42:20,101] INFO Parsing run SRR21799220 [2023-08-19 15:42:20,508] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:20,508] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:22,444] INFO Parsing run SRR21799221 [2023-08-19 15:42:22,851] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:22,852] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:24,727] INFO Parsing sample SRS15319015 [2023-08-19 15:42:25,138] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:25,138] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:25,141] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:25,554] INFO Getting Experiment for SRS15319015 [2023-08-19 15:42:25,554] INFO Parsing Experiment SRX17793192 [2023-08-19 15:42:25,965] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:25,965] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:25,969] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:26,376] WARNING There are 2 runs for SRX17793192 [2023-08-19 15:42:26,376] INFO Parsing run SRR21799226 [2023-08-19 15:42:26,781] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:26,782] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:28,665] INFO Parsing run SRR21799227 [2023-08-19 15:42:29,076] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:29,076] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 15:42:31,326] INFO Parsing sample SRS15319015 [2023-08-19 15:42:31,327] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:31,327] INFO Getting Experiment for SRS15319015 [2023-08-19 15:42:31,327] INFO Parsing Experiment SRX17793192 [2023-08-19 15:42:31,329] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:31,329] WARNING There are 2 runs for SRX17793192 [2023-08-19 15:42:31,329] INFO Parsing run SRR21799226 [2023-08-19 15:42:31,569] INFO Parsing run SRR21799227 [2023-08-19 15:42:31,832] INFO Parsing sample SRS15319024 [2023-08-19 15:42:31,835] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:31,835] INFO Getting Experiment for SRS15319024 [2023-08-19 15:42:31,835] INFO Parsing Experiment SRX17793201 [2023-08-19 15:42:31,837] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 15:42:31,837] WARNING There are 2 runs for SRX17793201 [2023-08-19 15:42:31,838] INFO Parsing run SRR21799208 [2023-08-19 15:42:32,090] INFO Parsing run SRR21799209 [2023-08-19 15:42:32,161] ERROR 429 Client Error: Too Many Requests for url: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id=SRR21799209&retmode=xml [2023-08-19 15:42:32,161] ERROR Provided accession is invalid usage: ffq [-h] [-o OUT] [-l LEVEL] [--ftp] [--aws] [--gcp] [--ncbi] [--split] [--verbose] [--version] IDs [IDs ...] ffq: error: For possible failure modes, please see https://github.com/pachterlab/ffq#failure-modes

ffq -o ./json_file/nar.json 10.1093/nar/gkac908 --verbose

Output: [2023-08-19 16:09:47,143] DEBUG Printing verbose output [2023-08-19 16:09:47,143] DEBUG Namespace(IDs=['10.1093/nar/gkac908'], o='./json_file/nar.json', t=None, l=None, ftp=False, aws=False, gcp=False, ncbi=False, split=False, verbose=True) [2023-08-19 16:09:47,143] WARNING Searching by DOI may result in missing information. [2023-08-19 16:09:47,143] INFO Searching for DOI '10.1093/NAR/GKAC908' [2023-08-19 16:09:47,245] INFO Searching for Study SRP with title 'Estrogen regulates divergent transcriptional and epigenetic cell states in breast cancer' [2023-08-19 16:09:48,612] WARNING No studies found with the given title. Searching Pubmed for DOI '10.1093/NAR/GKAC908' [2023-08-19 16:09:48,880] INFO Searching for GEO record linked to Pubmed ID '36318267' [2023-08-19 16:09:49,226] INFO Found 1 GEO Accessions: GSE154873 [2023-08-19 16:09:50,232] INFO Parsing GEO GSE154873 [2023-08-19 16:09:50,413] INFO Finding supplementary files for GEO GSE154873 [2023-08-19 16:09:52,959] WARNING There are 14 samples for GSE154873 [2023-08-19 16:09:52,959] INFO Parsing GSM GSM4681761 [2023-08-19 16:09:53,417] INFO Finding supplementary files for GSM GSM4681761 [2023-08-19 16:09:55,289] INFO Getting sample for GSM4681761 [2023-08-19 16:09:55,898] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:09:55,898] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:09:55,901] INFO Parsing sample SRS7054554 [2023-08-19 16:09:56,315] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:09:56,316] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:09:56,319] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:09:56,723] WARNING No experiment found [2023-08-19 16:09:56,723] INFO Getting Experiment for SRS7054554 [2023-08-19 16:09:57,192] INFO Parsing Experiment SRX8785938 [2023-08-19 16:09:57,196] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:09:57,601] WARNING There are 0 runs for SRX8785938 [2023-08-19 16:09:57,601] INFO Parsing GSM GSM4681762 [2023-08-19 16:09:57,815] INFO Finding supplementary files for GSM GSM4681762 [2023-08-19 16:09:59,995] INFO Getting sample for GSM4681762 [2023-08-19 16:10:00,555] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:00,555] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:00,557] INFO Parsing sample SRS7054555 [2023-08-19 16:10:00,973] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:00,973] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:00,976] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:01,381] WARNING No experiment found [2023-08-19 16:10:01,382] INFO Getting Experiment for SRS7054555 [2023-08-19 16:10:01,780] INFO Parsing Experiment SRX8785939 [2023-08-19 16:10:01,784] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:02,190] WARNING There are 0 runs for SRX8785939 [2023-08-19 16:10:02,190] INFO Parsing GSM GSM4681763 [2023-08-19 16:10:02,424] INFO Finding supplementary files for GSM GSM4681763 [2023-08-19 16:10:03,940] INFO Getting sample for GSM4681763 [2023-08-19 16:10:04,503] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:04,504] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:04,506] INFO Parsing sample SRS7054556 [2023-08-19 16:10:04,930] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:04,930] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:04,933] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:05,344] WARNING No experiment found [2023-08-19 16:10:05,344] INFO Getting Experiment for SRS7054556 [2023-08-19 16:10:05,742] INFO Parsing Experiment SRX8785940 [2023-08-19 16:10:05,746] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:06,154] WARNING There are 0 runs for SRX8785940 [2023-08-19 16:10:06,155] INFO Parsing GSM GSM4681764 [2023-08-19 16:10:06,386] INFO Finding supplementary files for GSM GSM4681764 [2023-08-19 16:10:07,928] INFO Getting sample for GSM4681764 [2023-08-19 16:10:08,482] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:08,483] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:08,485] INFO Parsing sample SRS7054557 [2023-08-19 16:10:08,898] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:08,898] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:08,900] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:09,303] WARNING No experiment found [2023-08-19 16:10:09,303] INFO Getting Experiment for SRS7054557 [2023-08-19 16:10:09,795] INFO Parsing Experiment SRX8785941 [2023-08-19 16:10:09,799] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:10,211] WARNING There are 0 runs for SRX8785941 [2023-08-19 16:10:10,211] INFO Parsing GSM GSM4681765 [2023-08-19 16:10:10,439] INFO Finding supplementary files for GSM GSM4681765 [2023-08-19 16:10:11,943] INFO Getting sample for GSM4681765 [2023-08-19 16:10:12,496] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:12,496] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:12,499] INFO Parsing sample SRS7054558 [2023-08-19 16:10:12,907] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:12,908] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:12,911] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:13,314] WARNING No experiment found [2023-08-19 16:10:13,314] INFO Getting Experiment for SRS7054558 [2023-08-19 16:10:13,676] INFO Parsing Experiment SRX8785942 [2023-08-19 16:10:13,681] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:14,088] WARNING There are 0 runs for SRX8785942 [2023-08-19 16:10:14,088] INFO Parsing GSM GSM6418438 [2023-08-19 16:10:14,288] INFO Finding supplementary files for GSM GSM6418438 [2023-08-19 16:10:15,626] INFO No supplementary files found for GSM6418438 [2023-08-19 16:10:15,999] INFO Getting sample for GSM6418438 [2023-08-19 16:10:16,633] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:16,634] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:16,636] INFO Parsing sample SRS14360572 [2023-08-19 16:10:17,039] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:17,040] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:17,043] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:17,446] INFO Getting Experiment for SRS14360572 [2023-08-19 16:10:17,446] INFO Parsing Experiment SRX16732252 [2023-08-19 16:10:17,449] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:17,855] WARNING There are 2 runs for SRX16732252 [2023-08-19 16:10:17,855] INFO Parsing run SRR20711356 [2023-08-19 16:10:18,260] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:18,260] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:20,138] INFO Parsing run SRR20711355 [2023-08-19 16:10:20,544] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:20,545] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:22,428] INFO Parsing GSM GSM6418439 [2023-08-19 16:10:23,090] INFO Finding supplementary files for GSM GSM6418439 [2023-08-19 16:10:24,182] INFO No supplementary files found for GSM6418439 [2023-08-19 16:10:24,692] INFO Getting sample for GSM6418439 [2023-08-19 16:10:25,245] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:25,245] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:25,247] INFO Parsing sample SRS14360573 [2023-08-19 16:10:25,652] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:25,653] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:25,656] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:26,062] INFO Getting Experiment for SRS14360573 [2023-08-19 16:10:26,062] INFO Parsing Experiment SRX16732253 [2023-08-19 16:10:26,066] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:26,491] WARNING There are 4 runs for SRX16732253 [2023-08-19 16:10:26,491] INFO Parsing run SRR20711357 [2023-08-19 16:10:26,902] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:26,902] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:28,868] INFO Parsing run SRR20711359 [2023-08-19 16:10:29,283] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:29,283] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:31,229] INFO Parsing run SRR20711358 [2023-08-19 16:10:31,641] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:31,642] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:33,682] INFO Parsing run SRR20711360 [2023-08-19 16:10:34,094] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:34,095] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:36,038] INFO Parsing GSM GSM6418440 [2023-08-19 16:10:36,903] INFO Finding supplementary files for GSM GSM6418440 [2023-08-19 16:10:38,072] INFO No supplementary files found for GSM6418440 [2023-08-19 16:10:38,444] INFO Getting sample for GSM6418440 [2023-08-19 16:10:39,518] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:39,519] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:39,520] INFO Parsing sample SRS14360574 [2023-08-19 16:10:39,937] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:39,937] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:39,940] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:40,344] INFO Getting Experiment for SRS14360574 [2023-08-19 16:10:40,344] INFO Parsing Experiment SRX16732254 [2023-08-19 16:10:40,349] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:40,762] WARNING There is 1 run for SRX16732254 [2023-08-19 16:10:40,762] INFO Parsing run SRR20711361 [2023-08-19 16:10:41,183] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:41,183] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:43,138] INFO Parsing GSM GSM6418441 [2023-08-19 16:10:43,890] INFO Finding supplementary files for GSM GSM6418441 [2023-08-19 16:10:44,994] INFO No supplementary files found for GSM6418441 [2023-08-19 16:10:45,413] INFO Getting sample for GSM6418441 [2023-08-19 16:10:46,000] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:46,001] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:46,003] INFO Parsing sample SRS14360575 [2023-08-19 16:10:46,417] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:46,418] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:46,420] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:46,832] INFO Getting Experiment for SRS14360575 [2023-08-19 16:10:46,832] INFO Parsing Experiment SRX16732255 [2023-08-19 16:10:46,836] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:47,241] WARNING There is 1 run for SRX16732255 [2023-08-19 16:10:47,241] INFO Parsing run SRR20711362 [2023-08-19 16:10:47,647] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:47,648] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:49,547] INFO Parsing GSM GSM6418442 [2023-08-19 16:10:49,766] INFO Finding supplementary files for GSM GSM6418442 [2023-08-19 16:10:50,855] INFO No supplementary files found for GSM6418442 [2023-08-19 16:10:51,245] INFO Getting sample for GSM6418442 [2023-08-19 16:10:51,819] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:51,819] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:51,821] INFO Parsing sample SRS14360576 [2023-08-19 16:10:52,236] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:52,236] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:52,238] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:52,650] INFO Getting Experiment for SRS14360576 [2023-08-19 16:10:52,650] INFO Parsing Experiment SRX16732256 [2023-08-19 16:10:52,653] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:53,061] WARNING There is 1 run for SRX16732256 [2023-08-19 16:10:53,061] INFO Parsing run SRR20711363 [2023-08-19 16:10:53,483] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:53,484] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:55,436] INFO Parsing GSM GSM6418443 [2023-08-19 16:10:55,646] INFO Finding supplementary files for GSM GSM6418443 [2023-08-19 16:10:56,767] INFO No supplementary files found for GSM6418443 [2023-08-19 16:10:57,188] INFO Getting sample for GSM6418443 [2023-08-19 16:10:58,203] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:58,204] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:58,206] INFO Parsing sample SRS14360577 [2023-08-19 16:10:58,617] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:58,617] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:58,620] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:59,039] INFO Getting Experiment for SRS14360577 [2023-08-19 16:10:59,039] INFO Parsing Experiment SRX16732257 [2023-08-19 16:10:59,043] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:10:59,458] WARNING There are 2 runs for SRX16732257 [2023-08-19 16:10:59,458] INFO Parsing run SRR20711365 [2023-08-19 16:10:59,883] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:10:59,883] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:01,814] INFO Parsing run SRR20711364 [2023-08-19 16:11:02,232] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:02,233] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:04,124] INFO Parsing GSM GSM6418444 [2023-08-19 16:11:04,337] INFO Finding supplementary files for GSM GSM6418444 [2023-08-19 16:11:05,427] INFO No supplementary files found for GSM6418444 [2023-08-19 16:11:06,217] INFO Getting sample for GSM6418444 [2023-08-19 16:11:07,075] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:07,076] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:07,078] INFO Parsing sample SRS14360578 [2023-08-19 16:11:07,485] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:07,486] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:07,488] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:11:07,891] INFO Getting Experiment for SRS14360578 [2023-08-19 16:11:07,892] INFO Parsing Experiment SRX16732258 [2023-08-19 16:11:07,897] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:11:08,300] WARNING There are 2 runs for SRX16732258 [2023-08-19 16:11:08,301] INFO Parsing run SRR20711366 [2023-08-19 16:11:08,712] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:08,713] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:10,618] INFO Parsing run SRR20711367 [2023-08-19 16:11:11,032] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:11,033] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:12,943] INFO Parsing GSM GSM6418445 [2023-08-19 16:11:13,141] INFO Finding supplementary files for GSM GSM6418445 [2023-08-19 16:11:14,232] INFO No supplementary files found for GSM6418445 [2023-08-19 16:11:15,152] INFO Getting sample for GSM6418445 [2023-08-19 16:11:15,699] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:15,700] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:15,702] INFO Parsing sample SRS14360579 [2023-08-19 16:11:16,115] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:16,115] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:16,118] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:11:16,523] INFO Getting Experiment for SRS14360579 [2023-08-19 16:11:16,524] INFO Parsing Experiment SRX16732259 [2023-08-19 16:11:16,526] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:11:16,939] WARNING There are 8 runs for SRX16732259 [2023-08-19 16:11:16,940] INFO Parsing run SRR20711374 [2023-08-19 16:11:17,359] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:17,359] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:19,432] INFO Parsing run SRR20711375 [2023-08-19 16:11:19,848] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:19,849] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:21,902] INFO Parsing run SRR20711368 [2023-08-19 16:11:22,312] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:22,312] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:24,435] INFO Parsing run SRR20711370 [2023-08-19 16:11:24,849] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:24,849] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:26,932] INFO Parsing run SRR20711371 [2023-08-19 16:11:27,358] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:27,359] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:29,574] INFO Parsing run SRR20711373 [2023-08-19 16:11:30,001] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:30,002] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:32,149] INFO Parsing run SRR20711369 [2023-08-19 16:11:32,581] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:32,581] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:34,850] INFO Parsing run SRR20711372 [2023-08-19 16:11:35,281] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:35,282] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:37,507] INFO Parsing GSM GSM6418446 [2023-08-19 16:11:37,730] INFO Finding supplementary files for GSM GSM6418446 [2023-08-19 16:11:39,076] INFO No supplementary files found for GSM6418446 [2023-08-19 16:11:39,536] INFO Getting sample for GSM6418446 [2023-08-19 16:11:40,159] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:40,162] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:40,165] INFO Parsing sample SRS14360580 [2023-08-19 16:11:40,597] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:40,597] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:40,601] WARNING Failed to parse sample information from ENA XML. Falling back to ENA search... [2023-08-19 16:11:41,012] INFO Getting Experiment for SRS14360580 [2023-08-19 16:11:41,012] INFO Parsing Experiment SRX16732260 [2023-08-19 16:11:41,020] WARNING Failed to parse experiment information from ENA XML. Falling back to ENA search... [2023-08-19 16:11:41,469] WARNING There are 8 runs for SRX16732260 [2023-08-19 16:11:41,469] INFO Parsing run SRR20711376 [2023-08-19 16:11:41,896] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:41,897] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:44,034] INFO Parsing run SRR20711377 [2023-08-19 16:11:44,457] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:44,458] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:46,581] INFO Parsing run SRR20711379 [2023-08-19 16:11:47,008] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:47,009] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:49,133] INFO Parsing run SRR20711380 [2023-08-19 16:11:49,559] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:49,560] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:51,665] INFO Parsing run SRR20711381 [2023-08-19 16:11:52,098] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:52,099] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:54,265] INFO Parsing run SRR20711382 [2023-08-19 16:11:54,701] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:54,702] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:56,834] INFO Parsing run SRR20711378 [2023-08-19 16:11:57,260] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:57,260] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:59,410] INFO Parsing run SRR20711383 [2023-08-19 16:11:59,832] DEBUG Encoding detection: utf_8 is most likely the one. [2023-08-19 16:11:59,833] DEBUG Encoding detection: utf_8 is most likely the one.

pachterlab / ffq

Question on ffq [DOIS] #61