Failure for workflow-microsalt-store-completed.sh

[henrikstranneheim]

Description

Cron hiseq.clinical@hasta $CRONIC ${PRODUCTION_HOME}/servers/resources/hasta.scilifelab.se/crontabs/workflow-microsalt-store-completed.sh >> ${LOG_BASE}/cg.workflow-microsalt-store-completed.log 2> >(tee -a ${LOG_BASE}/cg.workflow-microsalt-store-completed.log >&2)

Cronic detected failure for the command: /home/proj/production/servers/resources/hasta.scilifelab.se/crontabs/workflow-microsalt-store-completed.sh

2021-03-10 00:45:21 hasta.scilifelab.se cg.apps.hermes.models[155223] INFO Optional file /home/proj/production/microbial/queries/ACC7547A21/alignment/ACC7547A21_NC_045512.stats.ins not found, removing from bundle
2021-03-10 00:45:21 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing deliverables for case drivenbunny - 65 validation errors for CGDeliverables
files -> 0
 Mandatory file cannot be found at /home/proj/production/microbial/queries/sampleinfo.json (type=assertion_error)
files -> 4
 Mandatory file cannot be found at /home/proj/production/microbial/queries/config.log (type=assertion_error)
files -> 5
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A1/assembly/ACC7547A1_trimmed_contigs.fasta (type=assertion_error)
files -> 9
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A1/slurm_ACC7547A1.log (type=assertion_error)
files -> 11
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A1/alignment/ACC7547A1_NC_045512.bam_sort (type=assertion_error)
files -> 13
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A2/assembly/ACC7547A2_trimmed_contigs.fasta (type=assertion_error)
files -> 17
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A2/slurm_ACC7547A2.log (type=assertion_error)
files -> 19
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A2/alignment/ACC7547A2_NC_045512.bam_sort (type=assertion_error)
files -> 21
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A3/assembly/ACC7547A3_trimmed_contigs.fasta (type=assertion_error)
files -> 25
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A3/slurm_ACC7547A3.log (type=assertion_error)
files -> 27
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A3/alignment/ACC7547A3_NC_045512.bam_sort (type=assertion_error)
files -> 29
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A4/assembly/ACC7547A4_trimmed_contigs.fasta (type=assertion_error)
files -> 33
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A4/slurm_ACC7547A4.log (type=assertion_error)
files -> 35
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A4/alignment/ACC7547A4_NC_045512.bam_sort (type=assertion_error)
files -> 37
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A5/assembly/ACC7547A5_trimmed_contigs.fasta (type=assertion_error)
files -> 41
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A5/slurm_ACC7547A5.log (type=assertion_error)
files -> 43
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A5/alignment/ACC7547A5_NC_045512.bam_sort (type=assertion_error)
files -> 45
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A6/assembly/ACC7547A6_trimmed_contigs.fasta (type=assertion_error)
files -> 49
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A6/slurm_ACC7547A6.log (type=assertion_error)
files -> 51
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A6/alignment/ACC7547A6_NC_045512.bam_sort (type=assertion_error)
files -> 53
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A7/assembly/ACC7547A7_trimmed_contigs.fasta (type=assertion_error)
files -> 57
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A7/slurm_ACC7547A7.log (type=assertion_error)
files -> 59
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A7/alignment/ACC7547A7_NC_045512.bam_sort (type=assertion_error)
files -> 61
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A8/assembly/ACC7547A8_trimmed_contigs.fasta (type=assertion_error)
files -> 65
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A8/slurm_ACC7547A8.log (type=assertion_error)
files -> 67
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A8/alignment/ACC7547A8_NC_045512.bam_sort (type=assertion_error)
files -> 69
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A9/assembly/ACC7547A9_trimmed_contigs.fasta (type=assertion_error)
files -> 73
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A9/slurm_ACC7547A9.log (type=assertion_error)
files -> 75
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A9/alignment/ACC7547A9_NC_045512.bam_sort (type=assertion_error)
files -> 77
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A10/assembly/ACC7547A10_trimmed_contigs.fasta (type=assertion_error)
files -> 81
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A10/slurm_ACC7547A10.log (type=assertion_error)
files -> 83
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A10/alignment/ACC7547A10_NC_045512.bam_sort (type=assertion_error)
files -> 85
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A11/assembly/ACC7547A11_trimmed_contigs.fasta (type=assertion_error)
files -> 89
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A11/slurm_ACC7547A11.log (type=assertion_error)
files -> 91
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A11/alignment/ACC7547A11_NC_045512.bam_sort (type=assertion_error)
files -> 93
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A12/assembly/ACC7547A12_trimmed_contigs.fasta (type=assertion_error)
files -> 97
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A12/slurm_ACC7547A12.log (type=assertion_error)
files -> 99
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A12/alignment/ACC7547A12_NC_045512.bam_sort (type=assertion_error)
files -> 101
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A13/assembly/ACC7547A13_trimmed_contigs.fasta (type=assertion_error)
files -> 105
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A13/slurm_ACC7547A13.log (type=assertion_error)
files -> 107
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A13/alignment/ACC7547A13_NC_045512.bam_sort (type=assertion_error)
files -> 109
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A14/assembly/ACC7547A14_trimmed_contigs.fasta (type=assertion_error)
files -> 113
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A14/slurm_ACC7547A14.log (type=assertion_error)
files -> 115
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A14/alignment/ACC7547A14_NC_045512.bam_sort (type=assertion_error)
files -> 117
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A15/assembly/ACC7547A15_trimmed_contigs.fasta (type=assertion_error)
files -> 121
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A15/slurm_ACC7547A15.log (type=assertion_error)
files -> 123
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A15/alignment/ACC7547A15_NC_045512.bam_sort (type=assertion_error)
files -> 125
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A16/assembly/ACC7547A16_trimmed_contigs.fasta (type=assertion_error)
files -> 129
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A16/slurm_ACC7547A16.log (type=assertion_error)
files -> 131
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A16/alignment/ACC7547A16_NC_045512.bam_sort (type=assertion_error)
files -> 133
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A17/assembly/ACC7547A17_trimmed_contigs.fasta (type=assertion_error)
files -> 137
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A17/slurm_ACC7547A17.log (type=assertion_error)
files -> 139
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A17/alignment/ACC7547A17_NC_045512.bam_sort (type=assertion_error)
files -> 141
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A18/assembly/ACC7547A18_trimmed_contigs.fasta (type=assertion_error)
files -> 145
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A18/slurm_ACC7547A18.log (type=assertion_error)
files -> 147
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A18/alignment/ACC7547A18_NC_045512.bam_sort (type=assertion_error)
files -> 149
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A19/assembly/ACC7547A19_trimmed_contigs.fasta (type=assertion_error)
files -> 153
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A19/slurm_ACC7547A19.log (type=assertion_error)
files -> 155
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A19/alignment/ACC7547A19_NC_045512.bam_sort (type=assertion_error)
files -> 157
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A20/assembly/ACC7547A20_trimmed_contigs.fasta (type=assertion_error)
files -> 161
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A20/slurm_ACC7547A20.log (type=assertion_error)
files -> 163
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A20/alignment/ACC7547A20_NC_045512.bam_sort (type=assertion_error)
files -> 165
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A21/assembly/ACC7547A21_trimmed_contigs.fasta (type=assertion_error)
files -> 169
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A21/slurm_ACC7547A21.log (type=assertion_error)
files -> 171
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7547A21/alignment/ACC7547A21_NC_045512.bam_sort (type=assertion_error)
.
.
.
/home/proj/production/microbial/queries/ACC7548A20/alignment/ACC7548A20_NC_045512.stats.ins not found, removing from bundle
2021-03-10 00:45:22 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing deliverables for case restedguinea - 62 validation errors for CGDeliverables
files -> 0
 Mandatory file cannot be found at /home/proj/production/microbial/queries/sampleinfo.json (type=assertion_error)
files -> 4
 Mandatory file cannot be found at /home/proj/production/microbial/queries/config.log (type=assertion_error)
files -> 5
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A1/assembly/ACC7548A1_trimmed_contigs.fasta (type=assertion_error)
files -> 9
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A1/slurm_ACC7548A1.log (type=assertion_error)
files -> 11
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A1/alignment/ACC7548A1_NC_045512.bam_sort (type=assertion_error)
files -> 13
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A2/assembly/ACC7548A2_trimmed_contigs.fasta (type=assertion_error)
files -> 17
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A2/slurm_ACC7548A2.log (type=assertion_error)
files -> 19
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A2/alignment/ACC7548A2_NC_045512.bam_sort (type=assertion_error)
files -> 21
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A3/assembly/ACC7548A3_trimmed_contigs.fasta (type=assertion_error)
files -> 25
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A3/slurm_ACC7548A3.log (type=assertion_error)
files -> 27
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A3/alignment/ACC7548A3_NC_045512.bam_sort (type=assertion_error)
files -> 29
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A4/assembly/ACC7548A4_trimmed_contigs.fasta (type=assertion_error)
files -> 33
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A4/slurm_ACC7548A4.log (type=assertion_error)
files -> 35
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A4/alignment/ACC7548A4_NC_045512.bam_sort (type=assertion_error)
files -> 37
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A5/assembly/ACC7548A5_trimmed_contigs.fasta (type=assertion_error)
files -> 41
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A5/slurm_ACC7548A5.log (type=assertion_error)
files -> 43
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A5/alignment/ACC7548A5_NC_045512.bam_sort (type=assertion_error)
files -> 45
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A6/assembly/ACC7548A6_trimmed_contigs.fasta (type=assertion_error)
files -> 49
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A6/slurm_ACC7548A6.log (type=assertion_error)
files -> 51
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A6/alignment/ACC7548A6_NC_045512.bam_sort (type=assertion_error)
files -> 53
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A7/assembly/ACC7548A7_trimmed_contigs.fasta (type=assertion_error)
files -> 57
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A7/slurm_ACC7548A7.log (type=assertion_error)
files -> 59
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A7/alignment/ACC7548A7_NC_045512.bam_sort (type=assertion_error)
files -> 61
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A8/assembly/ACC7548A8_trimmed_contigs.fasta (type=assertion_error)
files -> 65
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A8/slurm_ACC7548A8.log (type=assertion_error)
files -> 67
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A8/alignment/ACC7548A8_NC_045512.bam_sort (type=assertion_error)
files -> 69
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A9/assembly/ACC7548A9_trimmed_contigs.fasta (type=assertion_error)
files -> 73
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A9/slurm_ACC7548A9.log (type=assertion_error)
files -> 75
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A9/alignment/ACC7548A9_NC_045512.bam_sort (type=assertion_error)
files -> 77
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A10/assembly/ACC7548A10_trimmed_contigs.fasta (type=assertion_error)
files -> 81
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A10/slurm_ACC7548A10.log (type=assertion_error)
files -> 83
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A10/alignment/ACC7548A10_NC_045512.bam_sort (type=assertion_error)
files -> 85
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A11/assembly/ACC7548A11_trimmed_contigs.fasta (type=assertion_error)
files -> 89
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A11/slurm_ACC7548A11.log (type=assertion_error)
files -> 91
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A11/alignment/ACC7548A11_NC_045512.bam_sort (type=assertion_error)
files -> 93
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A12/assembly/ACC7548A12_trimmed_contigs.fasta (type=assertion_error)
files -> 97
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A12/slurm_ACC7548A12.log (type=assertion_error)
files -> 99
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A12/alignment/ACC7548A12_NC_045512.bam_sort (type=assertion_error)
files -> 101
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A13/assembly/ACC7548A13_trimmed_contigs.fasta (type=assertion_error)
files -> 105
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A13/slurm_ACC7548A13.log (type=assertion_error)
files -> 107
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A13/alignment/ACC7548A13_NC_045512.bam_sort (type=assertion_error)
files -> 109
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A14/assembly/ACC7548A14_trimmed_contigs.fasta (type=assertion_error)
files -> 113
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A14/slurm_ACC7548A14.log (type=assertion_error)
files -> 115
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A14/alignment/ACC7548A14_NC_045512.bam_sort (type=assertion_error)
files -> 117
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A15/assembly/ACC7548A15_trimmed_contigs.fasta (type=assertion_error)
files -> 121
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A15/slurm_ACC7548A15.log (type=assertion_error)
files -> 123
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A15/alignment/ACC7548A15_NC_045512.bam_sort (type=assertion_error)
files -> 125
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A16/assembly/ACC7548A16_trimmed_contigs.fasta (type=assertion_error)
files -> 129
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A16/slurm_ACC7548A16.log (type=assertion_error)
files -> 131
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A16/alignment/ACC7548A16_NC_045512.bam_sort (type=assertion_error)
files -> 133
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A17/assembly/ACC7548A17_trimmed_contigs.fasta (type=assertion_error)
files -> 137
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A17/slurm_ACC7548A17.log (type=assertion_error)
files -> 139
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A17/alignment/ACC7548A17_NC_045512.bam_sort (type=assertion_error)
files -> 141
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A18/assembly/ACC7548A18_trimmed_contigs.fasta (type=assertion_error)
files -> 145
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A18/slurm_ACC7548A18.log (type=assertion_error)
files -> 147
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A18/alignment/ACC7548A18_NC_045512.bam_sort (type=assertion_error)
files -> 149
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A19/assembly/ACC7548A19_trimmed_contigs.fasta (type=assertion_error)
files -> 153
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A19/slurm_ACC7548A19.log (type=assertion_error)
files -> 155
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A19/alignment/ACC7548A19_NC_045512.bam_sort (type=assertion_error)
files -> 157
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A20/assembly/ACC7548A20_trimmed_contigs.fasta (type=assertion_error)
files -> 161
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A20/slurm_ACC7548A20.log (type=assertion_error)
files -> 163
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A20/alignment/ACC7548A20_NC_045512.bam_sort (type=assertion_error)
2021-03-10 00:45:22 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing restedguinea: 62 validation errors for CGDeliverables
files -> 0
 Mandatory file cannot be found at /home/proj/production/microbial/queries/sampleinfo.json (type=assertion_error)
files -> 4
 Mandatory file cannot be found at /home/proj/production/microbial/queries/config.log (type=assertion_error)
files -> 5
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A1/assembly/ACC7548A1_trimmed_contigs.fasta (type=assertion_error)
files -> 9
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A1/slurm_ACC7548A1.log (type=assertion_error)
files -> 11
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A1/alignment/ACC7548A1_NC_045512.bam_sort (type=assertion_error)
files -> 13
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A2/assembly/ACC7548A2_trimmed_contigs.fasta (type=assertion_error)
files -> 17
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A2/slurm_ACC7548A2.log (type=assertion_error)
files -> 19
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A2/alignment/ACC7548A2_NC_045512.bam_sort (type=assertion_error)
files -> 21
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A3/assembly/ACC7548A3_trimmed_contigs.fasta (type=assertion_error)
files -> 25
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A3/slurm_ACC7548A3.log (type=assertion_error)
files -> 27
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A3/alignment/ACC7548A3_NC_045512.bam_sort (type=assertion_error)
files -> 29
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A4/assembly/ACC7548A4_trimmed_contigs.fasta (type=assertion_error)
files -> 33
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A4/slurm_ACC7548A4.log (type=assertion_error)
files -> 35
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A4/alignment/ACC7548A4_NC_045512.bam_sort (type=assertion_error)
files -> 37
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A5/assembly/ACC7548A5_trimmed_contigs.fasta (type=assertion_error)
files -> 41
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A5/slurm_ACC7548A5.log (type=assertion_error)
files -> 43
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A5/alignment/ACC7548A5_NC_045512.bam_sort (type=assertion_error)
files -> 45
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A6/assembly/ACC7548A6_trimmed_contigs.fasta (type=assertion_error)
files -> 49
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A6/slurm_ACC7548A6.log (type=assertion_error)
files -> 51
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A6/alignment/ACC7548A6_NC_045512.bam_sort (type=assertion_error)
files -> 53
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A7/assembly/ACC7548A7_trimmed_contigs.fasta (type=assertion_error)
files -> 57
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A7/slurm_ACC7548A7.log (type=assertion_error)
files -> 59
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A7/alignment/ACC7548A7_NC_045512.bam_sort (type=assertion_error)
files -> 61
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A8/assembly/ACC7548A8_trimmed_contigs.fasta (type=assertion_error)
files -> 65
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A8/slurm_ACC7548A8.log (type=assertion_error)
files -> 67
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A8/alignment/ACC7548A8_NC_045512.bam_sort (type=assertion_error)
files -> 69
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A9/assembly/ACC7548A9_trimmed_contigs.fasta (type=assertion_error)
files -> 73
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A9/slurm_ACC7548A9.log (type=assertion_error)
files -> 75
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A9/alignment/ACC7548A9_NC_045512.bam_sort (type=assertion_error)
files -> 77
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A10/assembly/ACC7548A10_trimmed_contigs.fasta (type=assertion_error)
files -> 81
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A10/slurm_ACC7548A10.log (type=assertion_error)
files -> 83
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A10/alignment/ACC7548A10_NC_045512.bam_sort (type=assertion_error)
files -> 85
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A11/assembly/ACC7548A11_trimmed_contigs.fasta (type=assertion_error)
files -> 89
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A11/slurm_ACC7548A11.log (type=assertion_error)
files -> 91
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A11/alignment/ACC7548A11_NC_045512.bam_sort (type=assertion_error)
files -> 93
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A12/assembly/ACC7548A12_trimmed_contigs.fasta (type=assertion_error)
files -> 97
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A12/slurm_ACC7548A12.log (type=assertion_error)
files -> 99
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A12/alignment/ACC7548A12_NC_045512.bam_sort (type=assertion_error)
files -> 101
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A13/assembly/ACC7548A13_trimmed_contigs.fasta (type=assertion_error)
files -> 105
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A13/slurm_ACC7548A13.log (type=assertion_error)
files -> 107
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A13/alignment/ACC7548A13_NC_045512.bam_sort (type=assertion_error)
files -> 109
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A14/assembly/ACC7548A14_trimmed_contigs.fasta (type=assertion_error)
files -> 113
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A14/slurm_ACC7548A14.log (type=assertion_error)
files -> 115
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A14/alignment/ACC7548A14_NC_045512.bam_sort (type=assertion_error)
files -> 117
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A15/assembly/ACC7548A15_trimmed_contigs.fasta (type=assertion_error)
files -> 121
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A15/slurm_ACC7548A15.log (type=assertion_error)
files -> 123
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A15/alignment/ACC7548A15_NC_045512.bam_sort (type=assertion_error)
files -> 125
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A16/assembly/ACC7548A16_trimmed_contigs.fasta (type=assertion_error)
files -> 129
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A16/slurm_ACC7548A16.log (type=assertion_error)
files -> 131
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A16/alignment/ACC7548A16_NC_045512.bam_sort (type=assertion_error)
files -> 133
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A17/assembly/ACC7548A17_trimmed_contigs.fasta (type=assertion_error)
files -> 137
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A17/slurm_ACC7548A17.log (type=assertion_error)
files -> 139
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A17/alignment/ACC7548A17_NC_045512.bam_sort (type=assertion_error)
files -> 141
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A18/assembly/ACC7548A18_trimmed_contigs.fasta (type=assertion_error)
files -> 145
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A18/slurm_ACC7548A18.log (type=assertion_error)
files -> 147
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A18/alignment/ACC7548A18_NC_045512.bam_sort (type=assertion_error)
files -> 149
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A19/assembly/ACC7548A19_trimmed_contigs.fasta (type=assertion_error)
files -> 153
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A19/slurm_ACC7548A19.log (type=assertion_error)
files -> 155
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A19/alignment/ACC7548A19_NC_045512.bam_sort (type=assertion_error)
files -> 157
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A20/assembly/ACC7548A20_trimmed_contigs.fasta (type=assertion_error)
files -> 161
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A20/slurm_ACC7548A20.log (type=assertion_error)
files -> 163
 Mandatory file cannot be found at /home/proj/production/microbial/queries/ACC7548A20/alignment/ACC7548A20_NC_045512.bam_sort (type=assertion_error)
.
.
/home/proj/production/microbial/results//ACC7574_2021.3.8_18.49.4/ACC7574A88/alignment/ACC7574A88_NC_011751.1.stats.ins not found, removing from bundle
2021-03-10 00:45:23 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing deliverables for case legalgopher - 126 validation errors for CGDeliverables
files -> 45
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7574_2021.3.8_18.49.4/ACC7574A6/assembly/ACC7574A6_trimmed_contigs.fasta (type=assertion_error)
files -> 49
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7574_2021.3.8_18.49.4/ACC7574A6/slurm_ACC7574A6.log (type=assertion_error)
files -> 51
.
.
.2021-03-10 00:45:24 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing deliverables for case casualkoala - 6 validation errors for CGDeliverables
files -> 221
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A28/assembly/ACC7590A28_trimmed_contigs.fasta (type=assertion_error)
files -> 225
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A28/slurm_ACC7590A28.log (type=assertion_error)
files -> 227
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A28/alignment/ACC7590A28_NC_045512.bam_sort (type=assertion_error)
files -> 269
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A34/assembly/ACC7590A34_trimmed_contigs.fasta (type=assertion_error)
files -> 273
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A34/slurm_ACC7590A34.log (type=assertion_error)
files -> 275
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A34/alignment/ACC7590A34_NC_045512.bam_sort (type=assertion_error)
2021-03-10 00:45:24 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing casualkoala: 6 validation errors for CGDeliverables
files -> 221
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A28/assembly/ACC7590A28_trimmed_contigs.fasta (type=assertion_error)
files -> 225
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A28/slurm_ACC7590A28.log (type=assertion_error)
files -> 227
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A28/alignment/ACC7590A28_NC_045512.bam_sort (type=assertion_error)
files -> 269
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A34/assembly/ACC7590A34_trimmed_contigs.fasta (type=assertion_error)
files -> 273
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A34/slurm_ACC7590A34.log (type=assertion_error)
files -> 275
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7590_2021.2.15_12.20.52/ACC7590A34/alignment/ACC7590A34_NC_045512.bam_sort (type=assertion_error)
.
.
.
2021-03-10 00:45:25 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing deliverables for case humanesole - 21 validation errors for CGDeliverables
files -> 5
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A1/assembly/ACC7599A1_trimmed_contigs.fasta (type=assertion_error)
files -> 9
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A1/slurm_ACC7599A1.log (type=assertion_error)
files -> 11
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A1/alignment/ACC7599A1_NC_045512.bam_sort (type=assertion_error)
files -> 61
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A8/assembly/ACC7599A8_trimmed_contigs.fasta (type=assertion_error)
files -> 65
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A8/slurm_ACC7599A8.log (type=assertion_error)
files -> 67
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A8/alignment/ACC7599A8_NC_045512.bam_sort (type=assertion_error)
files -> 117
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A15/assembly/ACC7599A15_trimmed_contigs.fasta (type=assertion_error)
files -> 121
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A15/slurm_ACC7599A15.log (type=assertion_error)
files -> 123
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A15/alignment/ACC7599A15_NC_045512.bam_sort (type=assertion_error)
files -> 125
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A16/assembly/ACC7599A16_trimmed_contigs.fasta (type=assertion_error)
files -> 129
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A16/slurm_ACC7599A16.log (type=assertion_error)
files -> 131
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A16/alignment/ACC7599A16_NC_045512.bam_sort (type=assertion_error)
files -> 245
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A31/assembly/ACC7599A31_trimmed_contigs.fasta (type=assertion_error)
files -> 249
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A31/slurm_ACC7599A31.log (type=assertion_error)
files -> 251
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A31/alignment/ACC7599A31_NC_045512.bam_sort (type=assertion_error)
files -> 253
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A32/assembly/ACC7599A32_trimmed_contigs.fasta (type=assertion_error)
files -> 257
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A32/slurm_ACC7599A32.log (type=assertion_error)
files -> 259
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A32/alignment/ACC7599A32_NC_045512.bam_sort (type=assertion_error)
files -> 301
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A38/assembly/ACC7599A38_trimmed_contigs.fasta (type=assertion_error)
files -> 305
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A38/slurm_ACC7599A38.log (type=assertion_error)
files -> 307
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A38/alignment/ACC7599A38_NC_045512.bam_sort (type=assertion_error)
2021-03-10 00:45:25 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing humanesole: 21 validation errors for CGDeliverables
files -> 5
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A1/assembly/ACC7599A1_trimmed_contigs.fasta (type=assertion_error)
files -> 9
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A1/slurm_ACC7599A1.log (type=assertion_error)
files -> 11
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A1/alignment/ACC7599A1_NC_045512.bam_sort (type=assertion_error)
files -> 61
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A8/assembly/ACC7599A8_trimmed_contigs.fasta (type=assertion_error)
files -> 65
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A8/slurm_ACC7599A8.log (type=assertion_error)
files -> 67
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A8/alignment/ACC7599A8_NC_045512.bam_sort (type=assertion_error)
files -> 117
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A15/assembly/ACC7599A15_trimmed_contigs.fasta (type=assertion_error)
files -> 121
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A15/slurm_ACC7599A15.log (type=assertion_error)
files -> 123
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A15/alignment/ACC7599A15_NC_045512.bam_sort (type=assertion_error)
files -> 125
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A16/assembly/ACC7599A16_trimmed_contigs.fasta (type=assertion_error)
files -> 129
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A16/slurm_ACC7599A16.log (type=assertion_error)
files -> 131
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A16/alignment/ACC7599A16_NC_045512.bam_sort (type=assertion_error)
files -> 245
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A31/assembly/ACC7599A31_trimmed_contigs.fasta (type=assertion_error)
files -> 249
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A31/slurm_ACC7599A31.log (type=assertion_error)
files -> 251
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A31/alignment/ACC7599A31_NC_045512.bam_sort (type=assertion_error)
files -> 253
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A32/assembly/ACC7599A32_trimmed_contigs.fasta (type=assertion_error)
files -> 257
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A32/slurm_ACC7599A32.log (type=assertion_error)
files -> 259
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A32/alignment/ACC7599A32_NC_045512.bam_sort (type=assertion_error)
files -> 301
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A38/assembly/ACC7599A38_trimmed_contigs.fasta (type=assertion_error)
files -> 305
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A38/slurm_ACC7599A38.log (type=assertion_error)
files -> 307
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7599_2021.2.25_16.3.17/ACC7599A38/alignment/ACC7599A38_NC_045512.bam_sort (type=assertion_error)
.
.
.
2021-03-10 00:45:27 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing deliverables for case cuddlyimp - 24 validation errors for CGDeliverables
files -> 397
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A50/assembly/ACC7619A50_trimmed_contigs.fasta (type=assertion_error)
files -> 401
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A50/slurm_ACC7619A50.log (type=assertion_error)
files -> 403
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A50/alignment/ACC7619A50_NC_045512.bam_sort (type=assertion_error)
files -> 405
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A51/assembly/ACC7619A51_trimmed_contigs.fasta (type=assertion_error)
files -> 409
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A51/slurm_ACC7619A51.log (type=assertion_error)
files -> 411
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A51/alignment/ACC7619A51_NC_045512.bam_sort (type=assertion_error)
files -> 413
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A52/assembly/ACC7619A52_trimmed_contigs.fasta (type=assertion_error)
files -> 417
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A52/slurm_ACC7619A52.log (type=assertion_error)
files -> 419
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A52/alignment/ACC7619A52_NC_045512.bam_sort (type=assertion_error)
files -> 421
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A53/assembly/ACC7619A53_trimmed_contigs.fasta (type=assertion_error)
files -> 425
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A53/slurm_ACC7619A53.log (type=assertion_error)
files -> 427
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A53/alignment/ACC7619A53_NC_045512.bam_sort (type=assertion_error)
files -> 429
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A54/assembly/ACC7619A54_trimmed_contigs.fasta (type=assertion_error)
files -> 433
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A54/slurm_ACC7619A54.log (type=assertion_error)
files -> 435
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A54/alignment/ACC7619A54_NC_045512.bam_sort (type=assertion_error)
files -> 437
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A55/assembly/ACC7619A55_trimmed_contigs.fasta (type=assertion_error)
files -> 441
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A55/slurm_ACC7619A55.log (type=assertion_error)
files -> 443
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A55/alignment/ACC7619A55_NC_045512.bam_sort (type=assertion_error)
files -> 445
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A56/assembly/ACC7619A56_trimmed_contigs.fasta (type=assertion_error)
files -> 449
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A56/slurm_ACC7619A56.log (type=assertion_error)
files -> 451
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A56/alignment/ACC7619A56_NC_045512.bam_sort (type=assertion_error)
files -> 453
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A57/assembly/ACC7619A57_trimmed_contigs.fasta (type=assertion_error)
files -> 457
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A57/slurm_ACC7619A57.log (type=assertion_error)
files -> 459
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7619_2021.2.26_14.32.51/ACC7619A57/alignment/ACC7619A57_NC_045512.bam_sort (type=assertion_error)
.
.
.
2021-03-10 00:45:28 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing deliverables for case notedlynx - 66 validation errors for CGDeliverables
files -> 13
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7631_2021.2.26_12.46.1/ACC7631A2/assembly/ACC7631A2_trimmed_contigs.fasta (type=assertion_error)
files -> 17
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7631_2021.2.26_12.46.1/ACC7631A2/slurm_ACC7631A2.log (type=assertion_error)
files -> 19
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7631_2021.2.26_12.46.1/ACC7631A2/alignment/ACC7631A2_NC_045512.bam_sort (type=assertion_error)
.
.
.
2021-03-10 00:45:31 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing deliverables for case vitalkite - 3 validation errors for CGDeliverables
files -> 197
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7635_2021.3.2_20.5.26/ACC7635A25/assembly/ACC7635A25_trimmed_contigs.fasta (type=assertion_error)
files -> 201
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7635_2021.3.2_20.5.26/ACC7635A25/slurm_ACC7635A25.log (type=assertion_error)
files -> 203
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7635_2021.3.2_20.5.26/ACC7635A25/alignment/ACC7635A25_CP016017.1.bam_sort (type=assertion_error)
2021-03-10 00:45:31 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing vitalkite: 3 validation errors for CGDeliverables
files -> 197
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7635_2021.3.2_20.5.26/ACC7635A25/assembly/ACC7635A25_trimmed_contigs.fasta (type=assertion_error)
files -> 201
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7635_2021.3.2_20.5.26/ACC7635A25/slurm_ACC7635A25.log (type=assertion_error)
files -> 203
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7635_2021.3.2_20.5.26/ACC7635A25/alignment/ACC7635A25_CP016017.1.bam_sort (type=assertion_error)
.
.
.
2021-03-10 00:45:38 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing deliverables for case vocalgnat - 1 validation error for CGDeliverables
files -> 101
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7669_2021.3.8_13.55.49/ACC7669A13/assembly/ACC7669A13_trimmed_contigs.fasta (type=assertion_error)
2021-03-10 00:45:38 hasta.scilifelab.se cg.cli.workflow.commands[155223] ERROR Error storing vocalgnat: 1 validation error for CGDeliverables
files -> 101
 Mandatory file cannot be found at /home/proj/production/microbial/results//ACC7669_2021.3.8_13.55.49/ACC7669A13/assembly/ACC7669A13_trimmed_contigs.fasta (type=assertion_error)

This can be closed when

• [x] The crontab does not generate errors anymore

[henrikstranneheim]

@henningonsbring @talnor @sylvinite Could you have a look at this and try to correct these cases? Or let us know if there are code that needs to change in cg or hermes.

[talnor]

Quite a few of there have 0 reads in statusDB. So it seems like it is bad quality data that has not and will not be analysed.

[talnor]

/home/proj/production/microbial/queries/sampleinfo.json and /home/proj/production/microbial/queries/config.log have the wrong path.

In the deliverables file they are called "/home/proj/production/microbial/results/ACC7522_2021.3.10_10.50.46/sampleinfo.json". Does the naming need to updated in microSALT to be ticket_sampleinfo.json or do we update the paths in cg?

[sylvinite]

The missing file SAMPLE_trimmed_contigs.fasta is currently generated by the uSALT code https://github.com/Clinical-Genomics/microSALT/blob/master/microSALT/utils/job_creator.py#L208 However. Old samples that are being complained about, still need to be updated to "clear" the error status.

[henrikstranneheim]

I have not seen any crontab fails for this one for a while. Let close and reopen if needed.

[henningonsbring]

My solution to this was to rerun several microsalt cases, but since it seems to be fixed I wont start them.